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Opened 22 hours ago
Closed 8 hours ago
#20389 closed defect (duplicate)
Parsing BlastProtein results failed: HTTP Error 415: Unsupported Media Type
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-26.5-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6ete fromDatabase pdb format mmcif
Summary of feedback from opening 6ete fetched from pdb
---
notes | Fetching compressed mmCIF 6ete from http://files.rcsb.org/download/6ete.cif
Fetching CCD BWK from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/BWK/BWK.cif
6ete title:
Crystal structure of KDM4D with tetrazolhydrazide compound 5 [more info...]
Chain information for 6ete #1
---
Chain | Description | UniProt
A | Lysine-specific demethylase 4D | KDM4D_HUMAN 1-342
Non-standard residues in 6ete #1
---
BWK — [2-(1-methyl-1,2,3,4-tetrazol-4-ium-5-yl)ethanoylamino]azanium
EDO — 1,2-ethanediol (ethylene glycol)
NI — nickel (II) ion
SO4 — sulfate ion
ZN — zinc ion
569 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
3090 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> close #1
> open 6et6 fromDatabase pdb format mmcif
6et6 title:
Crystal structure of muramidase from Acinetobacter baumannii AB 5075UW
prophage [more info...]
Chain information for 6et6 #1
---
Chain | Description | UniProt
A | Lysozyme | A0A0D5YGK2_ACIBA 14-196
Non-standard residues in 6et6 #1
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
SO4 — sulfate ion
13 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
1378 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> open "/Users/gth_book/Documents/1_JOB_Files/Research_Proj_Prop/★
> Prop_2024_Enzybiotics ▲ 🌱/Structures_Analysis/Structures from
> PDB/AbLys1_8APP.cif"
AbLys1_8APP.cif title:
AbLys1 endolysin from Acinetobacter baumannii phage AbTZA1 [more info...]
Chain information for AbLys1_8APP.cif #2
---
Chain | Description | UniProt
A B C D | Endolysin | A0A3T0IGR7_9CAUD 1-187
Non-standard residues in AbLys1_8APP.cif #2
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
PO4 — phosphate ion
AbLys1_8APP.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
> close #2
> open "/Users/gth_book/Documents/1_JOB_Files/Research_Proj_Prop/★
> Prop_2024_Enzybiotics ▲ 🌱/Structures_Analysis/Structure
> analysis/AbLys1_8APP_monom.pdb"
Chain information for AbLys1_8APP_monom.pdb #2
---
Chain | Description
A | No description available
> hide #2 models
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6et6, chain A (#1) with AbLys1_8APP_monom.pdb, chain A (#2),
sequence alignment score = 597.2
RMSD between 94 pruned atom pairs is 0.530 angstroms; (across all 149 pairs:
4.699)
> show #2 models
> hide #2 models
> hide #1 models
> close #1
> ui tool show "Similar Structures"
> foldseek /A
Found 463 similar structures to AbLys1_8APP_monom.pdb #2/A in pdb database
using foldseek, name fs1
> show #2 models
> open 6et6
6et6 title:
Crystal structure of muramidase from Acinetobacter baumannii AB 5075UW
prophage [more info...]
Chain information for 6et6 #1
---
Chain | Description | UniProt
A | Lysozyme | A0A0D5YGK2_ACIBA 14-196
Non-standard residues in 6et6 #1
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
SO4 — sulfate ion
13 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
1378 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 3 N-terminal residues, 84 non-polymer residues more than 3.0 Angstroms
away.
Alignment of 6et6 chain A to query has RMSD 0.52 using 93 of 146 paired
residues within cutoff distance 2.0
> open 7m5i
7m5i title:
Endolysin from Escherichia coli O157:H7 phage FAHEc1 [more info...]
Chain information for 7m5i #3
---
Chain | Description | UniProt
A B | Endolysin | A0A0F6R9G3_9CAUD 1-154
Non-standard residues in 7m5i #3
---
PO4 — phosphate ion
7m5i mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2475 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 7 C-terminal residues, 5 N-terminal residues, 213 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 7m5i chain B to query has RMSD 0.911 using 107 of 146 paired
residues within cutoff distance 2.0
> hide #2 models
> show #2 models
> hide #1 models
> select #2/A:159
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> open 2anv
2anv title:
crystal structure of P22 lysozyme mutant L86M [more info...]
Chain information for 2anv #4
---
Chain | Description | UniProt
A B | Lysozyme | LYS_BPP22 1-146
Non-standard residues in 2anv #4
---
CL — chloride ion
IOD — iodide ion
MG — magnesium ion
SM — samarium (III) ion
SO4 — sulfate ion
2anv mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
3| software_defined_assembly
165 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2792 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 2 N-terminal residues, 378 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 2anv chain A to query has RMSD 1.04 using 129 of 144 paired
residues within cutoff distance 2.0
> open 4zpu
4zpu title:
The structure of DLP12 endolysin exhibits likely active and inactive
conformations. [more info...]
Chain information for 4zpu #5
---
Chain | Description | UniProt
A B C D | Lysozyme RrrD | LYSD_ECOLI 1-165
Non-standard residues in 4zpu #5
---
ACT — acetate ion
FMT — formic acid
4zpu mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Deleted 3 extra chains, 5 C-terminal residues, 19 N-terminal residues, 45 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 4zpu chain A to query has RMSD 0.855 using 87 of 135 paired
residues within cutoff distance 2.0
> open 8hp8
8hp8 title:
Crystal Structure of Engineered Endolysin EC340 derived from Gram-Negative
Bacteria targeted Bacteriophage [more info...]
Chain information for 8hp8 #6
---
Chain | Description
A B C | Endolysin mtEC340M
8hp8 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
Deleted 2 extra chains, 13 C-terminal residues, 2 N-terminal residues, 255
non-polymer residues more than 3.0 Angstroms away.
Alignment of 8hp8 chain C to query has RMSD 0.877 using 114 of 142 paired
residues within cutoff distance 2.0
> open 3hde
3hde title:
Crystal structure of full-length endolysin R21 from phage 21 [more info...]
Chain information for 3hde #7
---
Chain | Description | UniProt
A B C D | Lysozyme | LYS_BPP21 1-165
3hde mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Deleted 3 extra chains, 3 C-terminal residues, 19 N-terminal residues, 325
non-polymer residues more than 3.0 Angstroms away.
Alignment of 3hde chain C to query has RMSD 0.97 using 93 of 136 paired
residues within cutoff distance 2.0
> open 8b2s
8b2s title:
GH24 family muramidase from Trichophaea saccata with an SH3-like cell wall
binding domain [more info...]
Chain information for 8b2s #8
---
Chain | Description
A B | GH24 family muramidase
Non-standard residues in 8b2s #8
---
K — potassium ion
8b2s mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
3610 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 10 C-terminal residues, 79 N-terminal residues, 274
non-polymer residues more than 3.0 Angstroms away.
Alignment of 8b2s chain B to query has RMSD 0.925 using 101 of 145 paired
residues within cutoff distance 2.0
> open 1xjt
1xjt title:
Crystal structure of active form of P1 phage endolysin Lyz [more info...]
Chain information for 1xjt #9
---
Chain | Description | UniProt
A | Lysozyme | LYS_BPP1 1-185
Non-standard residues in 1xjt #9
---
CIT — citric acid
Deleted 8 C-terminal residues, 73 non-polymer residues more than 3.0 Angstroms
away.
Alignment of 1xjt chain A to query has RMSD 1 using 80 of 158 paired residues
within cutoff distance 2.0
> open 3hde
3hde title:
Crystal structure of full-length endolysin R21 from phage 21 [more info...]
Chain information for 3hde #10
---
Chain | Description | UniProt
A B C D | Lysozyme | LYS_BPP21 1-165
3hde mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Deleted 3 extra chains, 4 C-terminal residues, 19 N-terminal residues, 327
non-polymer residues more than 3.0 Angstroms away.
Alignment of 3hde chain D to query has RMSD 0.782 using 80 of 126 paired
residues within cutoff distance 2.0
> open 1jqu
1jqu title:
Are Carboxy Terminii of Helices Coded by the Local Sequence or by Tertiary
Structure Contacts [more info...]
Chain information for 1jqu #11
---
Chain | Description | UniProt
A B C D | Lysozyme | LYS_BPT4 1-164
1jqu mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
Deleted 3 extra chains, 11 C-terminal residues, 1 N-terminal residues, 23 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 1jqu chain C to query has RMSD 1.11 using 51 of 124 paired
residues within cutoff distance 2.0
> open 3fi5
3fi5 title:
Crystal Structure of T4 Lysozyme Mutant R96W [more info...]
Chain information for 3fi5 #12
---
Chain | Description | UniProt
A B C D | Lysozyme | LYS_BPT4 1-164
Non-standard residues in 3fi5 #12
---
CL — chloride ion
IPA — isopropyl alcohol (2-propanol)
NA — sodium ion
3fi5 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
360 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
5242 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 3 extra chains, 9 C-terminal residues, 2 N-terminal residues, 902 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 3fi5 chain C to query has RMSD 0.948 using 46 of 124 paired
residues within cutoff distance 2.0
> open 6a73
6a73 title:
Complex structure of CSN2 with IP6 [more info...]
Chain information for 6a73 #13
---
Chain | Description | UniProt
A B | COP9 signalosome complex subunit 2,Endolysin | CSN2_HUMAN 29-162, A0A097J809_BPT4 163-325
Non-standard residues in 6a73 #13
---
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)
SO4 — sulfate ion
6a73 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
4968 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 8 C-terminal residues, 95 N-terminal residues, 137
non-polymer residues more than 3.0 Angstroms away.
Alignment of 6a73 chain B to query has RMSD 1.17 using 64 of 153 paired
residues within cutoff distance 2.0
> open 192l
Summary of feedback from opening 192l fetched from pdb
---
note | Fetching compressed mmCIF 192l from http://files.rcsb.org/download/192l.cif
192l title:
A helix initiation signal In T4 lysozyme identified by polyalanine mutagenesis
[more info...]
Chain information for 192l #14
---
Chain | Description | UniProt
A | LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 192l #14
---
CL — chloride ion
HED — 2-hydroxyethyl disulfide
Deleted 7 C-terminal residues, 2 N-terminal residues, 56 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 192l chain A to query has RMSD 0.836 using 41 of 127 paired
residues within cutoff distance 2.0
> close
> open "/Users/gth_book/Documents/1_JOB_Files/Research_Proj_Prop/★
> Prop_2024_Enzybiotics ▲ 🌱/Structures_Analysis/Structure
> analysis/AbLys1_8APP_monom.pdb"
Chain information for AbLys1_8APP_monom.pdb #1
---
Chain | Description
A | No description available
> open 6et6
6et6 title:
Crystal structure of muramidase from Acinetobacter baumannii AB 5075UW
prophage [more info...]
Chain information for 6et6 #2
---
Chain | Description | UniProt
A | Lysozyme | A0A0D5YGK2_ACIBA 14-196
Non-standard residues in 6et6 #2
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
SO4 — sulfate ion
13 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
1378 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 3 N-terminal residues, 84 non-polymer residues more than 3.0 Angstroms
away.
> close #2
> foldseek /A
Found 404 similar structures to AbLys1_8APP_monom.pdb #1/A in pdb database
using foldseek, name fs2
> open 6et6
6et6 title:
Crystal structure of muramidase from Acinetobacter baumannii AB 5075UW
prophage [more info...]
Chain information for 6et6 #2
---
Chain | Description | UniProt
A | Lysozyme | A0A0D5YGK2_ACIBA 14-196
Non-standard residues in 6et6 #2
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
SO4 — sulfate ion
13 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
1378 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 3 N-terminal residues, 84 non-polymer residues more than 3.0 Angstroms
away.
Alignment of 6et6 chain A to query has RMSD 0.52 using 93 of 146 paired
residues within cutoff distance 2.0
> similarstructures sequences
> similarstructures traces
404 backbone traces
> close #3
> similarstructures cluster #1/A:131,64,88,177,69 clusterDistance 1.5
Clustered 392 of 404 hits that have the specified 5 residues into 2 groups
> similarstructures sequences
> color byattribute r:coverage #1/A palette 0,red:202,white:404,blue
1631 atoms, 342 residues, atom coverage range 1 to 404
> color byattribute r:conservation #1/A palette 0,blue:0.25,white:0.5,red
1631 atoms, 342 residues, atom conservation range 0.176 to 1
> color #1/A gray
> color #1/A & ::conservation>=0.5 red
> color byattribute r:lddt #1/A palette
> 0,red:0.2,orange:0.4,yellow:0.6,cornflowerblue:0.8,blue
1631 atoms, 342 residues, atom lddt range 0.337 to 1
7m5i title:
Endolysin from Escherichia coli O157:H7 phage FAHEc1 [more info...]
Chain information for 7m5i #3
---
Chain | Description | UniProt
A B | Endolysin | A0A0F6R9G3_9CAUD 1-154
Non-standard residues in 7m5i #3
---
PO4 — phosphate ion
7m5i mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2475 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 7 C-terminal residues, 5 N-terminal residues, 213 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 7m5i chain B to query has RMSD 0.911 using 107 of 146 paired
residues within cutoff distance 2.0
6h9d title:
Muramidase domain of SpmX from Asticaccaulis excentricus [more info...]
Chain information for 6h9d #4
---
Chain | Description | UniProt
A B C | Lysozyme | E8RMG8_ASTEC 2-150
Non-standard residues in 6h9d #4
---
CL — chloride ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
6h9d mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 2 extra chains, 2 N-terminal residues, 132 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 6h9d chain C to query has RMSD 0.804 using 99 of 145 paired
residues within cutoff distance 2.0
2anv title:
crystal structure of P22 lysozyme mutant L86M [more info...]
Chain information for 2anv #5
---
Chain | Description | UniProt
A B | Lysozyme | LYS_BPP22 1-146
Non-standard residues in 2anv #5
---
CL — chloride ion
IOD — iodide ion
MG — magnesium ion
SM — samarium (III) ion
SO4 — sulfate ion
2anv mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
3| software_defined_assembly
165 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2792 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 2 N-terminal residues, 378 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 2anv chain A to query has RMSD 1.04 using 129 of 144 paired
residues within cutoff distance 2.0
4zpu title:
The structure of DLP12 endolysin exhibits likely active and inactive
conformations. [more info...]
Chain information for 4zpu #6
---
Chain | Description | UniProt
A B C D | Lysozyme RrrD | LYSD_ECOLI 1-165
Non-standard residues in 4zpu #6
---
ACT — acetate ion
FMT — formic acid
4zpu mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Deleted 3 extra chains, 5 C-terminal residues, 19 N-terminal residues, 45 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 4zpu chain A to query has RMSD 0.855 using 87 of 135 paired
residues within cutoff distance 2.0
8hp8 title:
Crystal Structure of Engineered Endolysin EC340 derived from Gram-Negative
Bacteria targeted Bacteriophage [more info...]
Chain information for 8hp8 #7
---
Chain | Description
A B C | Endolysin mtEC340M
8hp8 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
Deleted 2 extra chains, 13 C-terminal residues, 2 N-terminal residues, 255
non-polymer residues more than 3.0 Angstroms away.
Alignment of 8hp8 chain C to query has RMSD 0.877 using 114 of 142 paired
residues within cutoff distance 2.0
3hde title:
Crystal structure of full-length endolysin R21 from phage 21 [more info...]
Chain information for 3hde #8
---
Chain | Description | UniProt
A B C D | Lysozyme | LYS_BPP21 1-165
3hde mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Deleted 3 extra chains, 3 C-terminal residues, 19 N-terminal residues, 325
non-polymer residues more than 3.0 Angstroms away.
Alignment of 3hde chain C to query has RMSD 0.97 using 93 of 136 paired
residues within cutoff distance 2.0
8b2s title:
GH24 family muramidase from Trichophaea saccata with an SH3-like cell wall
binding domain [more info...]
Chain information for 8b2s #9
---
Chain | Description
A B | GH24 family muramidase
Non-standard residues in 8b2s #9
---
K — potassium ion
8b2s mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
3610 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 10 C-terminal residues, 79 N-terminal residues, 274
non-polymer residues more than 3.0 Angstroms away.
Alignment of 8b2s chain B to query has RMSD 0.925 using 101 of 145 paired
residues within cutoff distance 2.0
1xjt title:
Crystal structure of active form of P1 phage endolysin Lyz [more info...]
Chain information for 1xjt #10
---
Chain | Description | UniProt
A | Lysozyme | LYS_BPP1 1-185
Non-standard residues in 1xjt #10
---
CIT — citric acid
Deleted 8 C-terminal residues, 73 non-polymer residues more than 3.0 Angstroms
away.
Alignment of 1xjt chain A to query has RMSD 1 using 80 of 158 paired residues
within cutoff distance 2.0
3hde title:
Crystal structure of full-length endolysin R21 from phage 21 [more info...]
Chain information for 3hde #11
---
Chain | Description | UniProt
A B C D | Lysozyme | LYS_BPP21 1-165
3hde mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Deleted 3 extra chains, 4 C-terminal residues, 19 N-terminal residues, 327
non-polymer residues more than 3.0 Angstroms away.
Alignment of 3hde chain D to query has RMSD 0.782 using 80 of 126 paired
residues within cutoff distance 2.0
1jqu title:
Are Carboxy Terminii of Helices Coded by the Local Sequence or by Tertiary
Structure Contacts [more info...]
Chain information for 1jqu #12
---
Chain | Description | UniProt
A B C D | Lysozyme | LYS_BPT4 1-164
1jqu mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
Deleted 3 extra chains, 11 C-terminal residues, 1 N-terminal residues, 23 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 1jqu chain C to query has RMSD 1.11 using 51 of 124 paired
residues within cutoff distance 2.0
3fi5 title:
Crystal Structure of T4 Lysozyme Mutant R96W [more info...]
Chain information for 3fi5 #13
---
Chain | Description | UniProt
A B C D | Lysozyme | LYS_BPT4 1-164
Non-standard residues in 3fi5 #13
---
CL — chloride ion
IPA — isopropyl alcohol (2-propanol)
NA — sodium ion
3fi5 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
360 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
5242 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 3 extra chains, 9 C-terminal residues, 2 N-terminal residues, 902 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 3fi5 chain C to query has RMSD 0.948 using 46 of 124 paired
residues within cutoff distance 2.0
6a73 title:
Complex structure of CSN2 with IP6 [more info...]
Chain information for 6a73 #14
---
Chain | Description | UniProt
A B | COP9 signalosome complex subunit 2,Endolysin | CSN2_HUMAN 29-162, A0A097J809_BPT4 163-325
Non-standard residues in 6a73 #14
---
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)
SO4 — sulfate ion
6a73 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
4968 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 8 C-terminal residues, 95 N-terminal residues, 137
non-polymer residues more than 3.0 Angstroms away.
Alignment of 6a73 chain B to query has RMSD 1.17 using 64 of 153 paired
residues within cutoff distance 2.0
192l title:
A helix initiation signal In T4 lysozyme identified by polyalanine mutagenesis
[more info...]
Chain information for 192l #15
---
Chain | Description | UniProt
A | LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 192l #15
---
CL — chloride ion
HED — 2-hydroxyethyl disulfide
Deleted 7 C-terminal residues, 2 N-terminal residues, 56 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 192l chain A to query has RMSD 0.836 using 41 of 127 paired
residues within cutoff distance 2.0
137l title:
Structural basis of amino acid α helix propensity [more info...]
Chain information for 137l #16
---
Chain | Description | UniProt
A B | T4 LYSOZYME | LYS_BPT4 1-164
137l mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Deleted 1 extra chains, 11 C-terminal residues, 2 N-terminal residues, 186
non-polymer residues more than 3.0 Angstroms away.
Alignment of 137l chain B to query has RMSD 0.973 using 49 of 125 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 5vnq from http://files.rcsb.org/download/5vnq.cif
Atom D1 is not in the residue template for MET /A:1
Atom D is not in the residue template for ASN /A:2
Atom D is not in the residue template for ILE /A:3
Atom D is not in the residue template for PHE /A:4
Atom D is not in the residue template for GLU /A:5
Atom D is not in the residue template for MET /A:6
Atom D is not in the residue template for LEU /A:7
Atom D is not in the residue template for ARG /A:8
Atom D is not in the residue template for ILE /A:9
Too many hydrogens missing from residue template(s) to warn about
5vnq title:
Neutron crystallographic structure of perdeuterated T4 lysozyme cysteine-free
pseudo-wild type at cryogenic temperature [more info...]
Chain information for 5vnq #17
---
Chain | Description | UniProt
A | Endolysin | D9IEF7_BPT4 1-164
Non-standard residues in 5vnq #17
---
CL — chloride ion
656 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 11 C-terminal residues, 2 N-terminal residues, 4 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 5vnq chain A to query has RMSD 0.995 using 48 of 126 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 5kim from http://files.rcsb.org/download/5kim.cif
Fetching CCD PHI from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/I/PHI/PHI.cif
5kim title:
Pseudo T4 lysozyme mutant - Y88PHE-I [more info...]
Chain information for 5kim #18
---
Chain | Description | UniProt
A | Endolysin | ENLYS_BPT4 1-164
Non-standard residues in 5kim #18
---
HED — 2-hydroxyethyl disulfide
NA — sodium ion
138 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 9 C-terminal residues, 2 N-terminal residues, 204 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 5kim chain A to query has RMSD 0.968 using 49 of 124 paired
residues within cutoff distance 2.0
5jgx title:
Spin-Labeled T4 Lysozyme Construct V131V1 [more info...]
Chain information for 5jgx #19
---
Chain | Description | UniProt
A | Endolysin | ENLYS_BPT4 1-164
Non-standard residues in 5jgx #19
---
CL — chloride ion
K — potassium ion
PO4 — phosphate ion
V1A — S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-imidazol-4-yl)
methanesulfonothioate
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 11 C-terminal residues, 2 N-terminal residues, 162 non-polymer
residues more than 3.0 Angstroms away.
Alignment of 5jgx chain A to query has RMSD 0.993 using 50 of 124 paired
residues within cutoff distance 2.0
3hdf title:
Crystal structure of truncated endolysin R21 from phage 21 [more info...]
Chain information for 3hdf #20
---
Chain | Description | UniProt
A B | Lysozyme | LYS_BPP21 27-165
Non-standard residues in 3hdf #20
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
NO3 — nitrate ion
3hdf mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
17 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 1 C-terminal residues, 3 N-terminal residues, 245 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 3hdf chain B to query has RMSD 1.17 using 67 of 124 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 2o79 from http://files.rcsb.org/download/2o79.cif
2o79 title:
T4 lysozyme with C-terminal extension [more info...]
Chain information for 2o79 #21
---
Chain | Description | UniProt
A | Lysozyme | LYS_BPT4 1-164
Non-standard residues in 2o79 #21
---
CL — chloride ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
PO4 — phosphate ion
31 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 9 C-terminal residues, 2 N-terminal residues, 113 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 2o79 chain A to query has RMSD 1 using 50 of 125 paired residues
within cutoff distance 2.0
Fetching compressed mmCIF 216l from http://files.rcsb.org/download/216l.cif
216l title:
Structural basis of α-helix propensity At two sites In T4 lysozyme [more
info...]
Chain information for 216l #22
---
Chain | Description | UniProt
A B | T4 LYSOZYME | LYS_BPT4 1-164
216l mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Deleted 1 extra chains, 11 C-terminal residues, 2 N-terminal residues, 14 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 216l chain B to query has RMSD 0.964 using 47 of 122 paired
residues within cutoff distance 2.0
5jgu title:
Spin-Labeled T4 Lysozyme Construct R119V1 [more info...]
Chain information for 5jgu #23
---
Chain | Description | UniProt
A | Endolysin | ENLYS_BPT4 1-164
Non-standard residues in 5jgu #23
---
CL — chloride ion
K — potassium ion
PO4 — phosphate ion
V1A — S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-imidazol-4-yl)
methanesulfonothioate
42 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 11 C-terminal residues, 2 N-terminal residues, 157 non-polymer
residues more than 3.0 Angstroms away.
Alignment of 5jgu chain A to query has RMSD 0.984 using 50 of 125 paired
residues within cutoff distance 2.0
4arj title:
Crystal structure of a pesticin (translocation and receptor binding domain)
from Y. pestis and T4-lysozyme chimera [more info...]
Chain information for 4arj #24
---
Chain | Description | UniProt
A B | PESTICIN, LYSOZYME | Q57159_YERPE 1-167, LYS_BPT4 169-331
Non-standard residues in 4arj #24
---
SO4 — sulfate ion
4arj mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
11 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
5079 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 14 C-terminal residues, 136 N-terminal residues, 57
non-polymer residues more than 3.0 Angstroms away.
Alignment of 4arj chain B to query has RMSD 0.996 using 59 of 140 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 3sb6 from http://files.rcsb.org/download/3sb6.cif
Fetching CCD CU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/CU/CU.cif
3sb6 title:
Cu-mediated Dimer of T4 Lysozyme D61H/K65H/R76H/R80H by Synthetic
Symmetrization [more info...]
Chain information for 3sb6 #25
---
Chain | Description | UniProt
A B | Lysozyme | LYS_BPT4 1-162
Non-standard residues in 3sb6 #25
---
CL — chloride ion
CU — copper (II) ion
2536 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 9 C-terminal residues, 4 N-terminal residues, 19 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 3sb6 chain A to query has RMSD 0.957 using 46 of 127 paired
residues within cutoff distance 2.0
137l title:
Structural basis of amino acid α helix propensity [more info...]
Chain information for 137l #26
---
Chain | Description | UniProt
A B | T4 LYSOZYME | LYS_BPT4 1-164
137l mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Deleted 1 extra chains, 9 C-terminal residues, 2 N-terminal residues, 168 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 137l chain A to query has RMSD 1 using 49 of 125 paired residues
within cutoff distance 2.0
Fetching compressed mmCIF 2q9d from http://files.rcsb.org/download/2q9d.cif
2q9d title:
Structure of spin-labeled T4 lysozyme mutant A41R1 [more info...]
Chain information for 2q9d #27
---
Chain | Description | UniProt
A | Lysozyme | LYS_BPT4 1-164
Non-standard residues in 2q9d #27
---
BME — β-mercaptoethanol
MTN — S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl]
methanesulfonothioate (MTSL)
1556 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 11 C-terminal residues, 2 N-terminal residues, 99 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 2q9d chain A to query has RMSD 1.03 using 51 of 124 paired
residues within cutoff distance 2.0
217l title:
Structural basis of α-helix propensity At two sites In T4 lysozyme [more
info...]
Chain information for 217l #28
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYCV_BPT4 1-164
Non-standard residues in 217l #28
---
BME — β-mercaptoethanol
CL — chloride ion
Deleted 9 C-terminal residues, 2 N-terminal residues, 86 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 217l chain A to query has RMSD 0.98 using 48 of 124 paired
residues within cutoff distance 2.0
201l title:
How amino-acid insertions are allowed In an α-helix of T4 lysozyme [more
info...]
Chain information for 201l #29
---
Chain | Description | UniProt
A B | T4 LYSOZYME | LYCV_BPT4 1-164
Non-standard residues in 201l #29
---
BME — β-mercaptoethanol
201l mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Deleted 1 extra chains, 11 C-terminal residues, 2 N-terminal residues, 85 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 201l chain B to query has RMSD 0.984 using 50 of 125 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 6pgz from http://files.rcsb.org/download/6pgz.cif
6pgz title:
MTSL labelled T4 lysozyme pseudo-wild type V75C mutant [more info...]
Chain information for 6pgz #30
---
Chain | Description | UniProt
A B | Endolysin | D9IEF7_BPT4 1-164
Non-standard residues in 6pgz #30
---
CL — chloride ion
MTN — S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl]
methanesulfonothioate (MTSL)
6pgz mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Deleted 1 extra chains, 9 C-terminal residues, 2 N-terminal residues, 51 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 6pgz chain B to query has RMSD 0.999 using 48 of 124 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 5ki1 from http://files.rcsb.org/download/5ki1.cif
5ki1 title:
Pseudo T4 lysozyme mutant - Y18F [more info...]
Chain information for 5ki1 #31
---
Chain | Description | UniProt
A | Endolysin | ENLYS_BPT4 1-164
Non-standard residues in 5ki1 #31
---
HED — 2-hydroxyethyl disulfide
22 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 9 C-terminal residues, 2 N-terminal residues, 161 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 5ki1 chain A to query has RMSD 1.01 using 49 of 126 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 5jgn from http://files.rcsb.org/download/5jgn.cif
5jgn title:
Spin-Labeled T4 Lysozyme Construct I9V1 [more info...]
Chain information for 5jgn #32
---
Chain | Description | UniProt
A | Endolysin | ENLYS_BPT4 1-164
Non-standard residues in 5jgn #32
---
CL — chloride ion
K — potassium ion
PO4 — phosphate ion
V1A — S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-imidazol-4-yl)
methanesulfonothioate
33 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 11 C-terminal residues, 2 N-terminal residues, 168 non-polymer
residues more than 3.0 Angstroms away.
Alignment of 5jgn chain A to query has RMSD 0.959 using 49 of 124 paired
residues within cutoff distance 2.0
1t97 title:
Use of sequence duplication to engineer a ligand-triggered long-distance
molecular switch in T4 Lysozyme [more info...]
Chain information for 1t97 #33
---
Chain | Description | UniProt
A B | Lysozyme | LYS_BPT4 1-175
1t97 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Deleted 1 extra chains, 9 C-terminal residues, 2 N-terminal residues, 55 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 1t97 chain B to query has RMSD 1.01 using 50 of 129 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 1l73 from http://files.rcsb.org/download/1l73.cif
1l73 title:
Multiple stabilizing alanine replacements within α-helix 126-134 of T4
lysozyme have independent, additive effects on both structure and stability
[more info...]
Chain information for 1l73 #34
---
Chain | Description | UniProt
A | LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 1l73 #34
---
BME — β-mercaptoethanol
CL — chloride ion
Deleted 9 C-terminal residues, 2 N-terminal residues, 76 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1l73 chain A to query has RMSD 0.93 using 44 of 124 paired
residues within cutoff distance 2.0
1epy title:
T4 lysozyme mutant, T21H/C54T/C97A/Q141H/T142H [more info...]
Chain information for 1epy #35
---
Chain | Description | UniProt
A | LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 1epy #35
---
CL — chloride ion
CO — cobalt (II) ion
SO4 — sulfate ion
Deleted 9 C-terminal residues, 2 N-terminal residues, 44 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1epy chain A to query has RMSD 0.924 using 45 of 127 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 168l from http://files.rcsb.org/download/168l.cif
168l title:
Protein flexibility and adaptability seen In 25 crystal forms of T4 lysozyme
[more info...]
Chain information for 168l #36
---
Chain | Description | UniProt
A B C D E | T4 LYSOZYME | LYS_BPT4 1-164
168l mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
5| author_defined_assembly
Deleted 4 extra chains, 11 C-terminal residues, 2 N-terminal residues.
Alignment of 168l chain B to query has RMSD 1.18 using 67 of 125 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 6v51 from http://files.rcsb.org/download/6v51.cif
Fetching CCD QPM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/QPM/QPM.cif
6v51 title:
Spin-labeled T4 Lysozyme (9/131FnbY)-(4-Amino-TEMPO) [more info...]
Chain information for 6v51 #37
---
Chain | Description | UniProt
A | Endolysin | D9IEF7_BPT4 1-164
Non-standard residues in 6v51 #37
---
QPM — 4-amino-2,2,6,6-tetramethylpiperidin-1-ol (4-Amino-TEMPO)
12 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 11 C-terminal residues, 2 N-terminal residues, 83 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 6v51 chain A to query has RMSD 0.927 using 48 of 126 paired
residues within cutoff distance 2.0
4arj title:
Crystal structure of a pesticin (translocation and receptor binding domain)
from Y. pestis and T4-lysozyme chimera [more info...]
Chain information for 4arj #38
---
Chain | Description | UniProt
A B | PESTICIN, LYSOZYME | Q57159_YERPE 1-167, LYS_BPT4 169-331
Non-standard residues in 4arj #38
---
SO4 — sulfate ion
4arj mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
11 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
5079 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 14 C-terminal residues, 137 N-terminal residues, 61
non-polymer residues more than 3.0 Angstroms away.
Alignment of 4arj chain A to query has RMSD 0.987 using 54 of 136 paired
residues within cutoff distance 2.0
2hum title:
Crystal structure of T4 Lysozyme D72C synthetic dimer [more info...]
Chain information for 2hum #39
---
Chain | Description | UniProt
A B | Lysozyme | LYS_BPT4 1-164
Non-standard residues in 2hum #39
---
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)
Deleted 1 extra chains, 11 C-terminal residues, 2 N-terminal residues, 61 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 2hum chain A to query has RMSD 0.953 using 49 of 125 paired
residues within cutoff distance 2.0
1l26 title:
Replacements of PRO86 In phage T4 lysozyme extend an α-helix but do not alter
protein stability [more info...]
Chain information for 1l26 #40
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 1l26 #40
---
BME — β-mercaptoethanol
1 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 11 C-terminal residues, 2 N-terminal residues, 60 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1l26 chain A to query has RMSD 1.06 using 49 of 125 paired
residues within cutoff distance 2.0
1l77 title:
Design and structural analysis of alternative hydrophobic core packing
arrangements In bacteriophage T4 lysozyme [more info...]
Chain information for 1l77 #41
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYCV_BPT4 1-164
Non-standard residues in 1l77 #41
---
BME — β-mercaptoethanol
CL — chloride ion
Deleted 7 C-terminal residues, 2 N-terminal residues, 38 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1l77 chain A to query has RMSD 0.983 using 49 of 127 paired
residues within cutoff distance 2.0
1l75 title:
Multiple stabilizing alanine replacements within α-helix 126-134 of T4
lysozyme have independent, additive effects on both structure and stability
[more info...]
Chain information for 1l75 #42
---
Chain | Description | UniProt
A | LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 1l75 #42
---
BME — β-mercaptoethanol
CL — chloride ion
Deleted 9 C-terminal residues, 2 N-terminal residues, 73 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1l75 chain A to query has RMSD 0.852 using 42 of 127 paired
residues within cutoff distance 2.0
175l title:
Protein flexibility and adaptability seen In 25 crystal forms of T4 lysozyme
[more info...]
Chain information for 175l #43
---
Chain | Description | UniProt
A B | T4 LYSOZYME | LYS_BPT4 1-164
175l mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Deleted 1 extra chains, 11 C-terminal residues, 2 N-terminal residues, 58 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 175l chain B to query has RMSD 0.922 using 46 of 127 paired
residues within cutoff distance 2.0
145l title:
Role of backbone flexibility In the accommodation of variants that repack the
core of T4 lysozyme [more info...]
Chain information for 145l #44
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYCV_BPT4 1-164
Non-standard residues in 145l #44
---
BME — β-mercaptoethanol
Deleted 9 C-terminal residues, 2 N-terminal residues, 34 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 145l chain A to query has RMSD 0.931 using 49 of 125 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 6cm4 from http://files.rcsb.org/download/6cm4.cif
Fetching CCD 8NU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/8NU/8NU.cif
Fetching CCD PEG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/PEG/PEG.cif
6cm4 title:
Structure of the D2 Dopamine Receptor Bound to the Atypical Antipsychotic Drug
Risperidone [more info...]
Chain information for 6cm4 #45
---
Chain | Description | UniProt
A | D(2) dopamine receptor, endolysin chimera | DRD2_HUMAN 35-222 362-443, D9IEF7_BPT4 1002-1161
Non-standard residues in 6cm4 #45
---
8NU —
3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one
OLA — oleic acid
PEG — di(hydroxyethyl)ether
2991 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 87 C-terminal residues, 184 N-terminal residues, 21 non-polymer
residues more than 3.0 Angstroms away.
Alignment of 6cm4 chain A to query has RMSD 1.02 using 55 of 126 paired
residues within cutoff distance 2.0
[deleted to fit within ticket limits]
Deleted 9 C-terminal residues, 2 N-terminal residues, 75 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1dyg chain A to query has RMSD 0.938 using 45 of 127 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 157l from http://files.rcsb.org/download/157l.cif
157l title:
Control of enzyme activity by an engineered disulfide bond [more info...]
Chain information for 157l #341
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYCV_BPT4 1-164
Non-standard residues in 157l #341
---
BME — β-mercaptoethanol
CL — chloride ion
Deleted 9 C-terminal residues, 2 N-terminal residues, 76 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 157l chain A to query has RMSD 0.978 using 47 of 127 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 6xyr from http://files.rcsb.org/download/6xyr.cif
6xyr title:
Structure of the T4Lnano fusion protein [more info...]
Chain information for 6xyr #342
---
Chain | Description | UniProt
A | T4Lnano,Endolysin,Calmodulin,Endolysin,Calmodulin-1 | ENLYS_BPT4 37-199, CALM1_HUMAN 214-361
Non-standard residues in 6xyr #342
---
CA — calcium ion
CL — chloride ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
Deleted 163 C-terminal residues, 34 N-terminal residues, 75 non-polymer
residues more than 3.0 Angstroms away.
Alignment of 6xyr chain A to query has RMSD 1.1 using 52 of 124 paired
residues within cutoff distance 2.0
222l title:
Generating ligand binding sites In T4 lysozyme using deficiency-creating
substitutions [more info...]
Chain information for 222l #343
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYCV_BPT4 1-164
Non-standard residues in 222l #343
---
BME — β-mercaptoethanol
CL — chloride ion
Deleted 9 C-terminal residues, 2 N-terminal residues, 70 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 222l chain A to query has RMSD 1.02 using 49 of 125 paired
residues within cutoff distance 2.0
174l title:
Protein flexibility and adaptability seen In 25 crystal forms of T4 lysozyme
[more info...]
Chain information for 174l #344
---
Chain | Description | UniProt
A B | T4 LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 174l #344
---
SO4 — sulfate ion
174l mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 9 C-terminal residues, 2 N-terminal residues, 32 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 174l chain B to query has RMSD 1.31 using 77 of 128 paired
residues within cutoff distance 2.0
6p5w title:
Structure of DCN1 bound to
3-methyl-N-((4S,5S)-3-methyl-6-oxo-1-phenyl-4-(p-tolyl)-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl)benzamide
[more info...]
Chain information for 6p5w #345
---
Chain | Description | UniProt
A | Lysozyme,DCN1-like protein 1 chimera | D9IEF7_BPT4 1-164, DCNL1_HUMAN 1062-1259
Non-standard residues in 6p5w #345
---
O0A —
3-methyl-N-[(4S,5S)-3-methyl-4-(4-methylphenyl)-6-oxo-1-phenyl-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl]benzamide
2996 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 204 C-terminal residues, 15 N-terminal residues, 200 non-polymer
residues more than 3.0 Angstroms away.
Alignment of 6p5w chain A to query has RMSD 1.11 using 55 of 121 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 6fw2 from http://files.rcsb.org/download/6fw2.cif
Fetching CCD MOO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/MOO/MOO.cif
6fw2 title:
Crystal Structure of human mARC1 [more info...]
Chain information for 6fw2 #346
---
Chain | Description | UniProt
A | Mitochondrial amidoxime-reducing component 1,Endolysin,Mitochondrial amidoxime-reducing component 1 | MARC1_HUMAN 53-128 131-336, D9IEF7_BPT4 1001-1161
Non-standard residues in 6fw2 #346
---
B3P — 2-[3-(2-hydroxy-1,1-dihydroxymethyl-
ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol
EFK — oxidanyl(oxidanylidene)molybdenum
MOO — molybdate ion (molybdate)
MTE — phosphonic
acidmono-(2-amino-5,6-dimercapto-4-oxo-3,7,8A,9,10,10A-hexahydro-4H-8-oxa-1,3,9,10-tetraaza-
anthracen-7-ylmethyl)ester
PO4 — phosphate ion
53 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 214 C-terminal residues, 79 N-terminal residues, 340 non-polymer
residues more than 3.0 Angstroms away.
Alignment of 6fw2 chain A to query has RMSD 0.933 using 47 of 127 paired
residues within cutoff distance 2.0
256l title:
Bacteriophage T4 lysozyme [more info...]
Chain information for 256l #347
---
Chain | Description | UniProt
A | LYSOZYME | LYS_BPT4 1-164
Deleted 11 C-terminal residues, 2 N-terminal residues, 64 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 256l chain A to query has RMSD 1.02 using 48 of 125 paired
residues within cutoff distance 2.0
247l title:
The response of T4 lysozyme to large-to-small substitutions within the core
and its relation to the hydrophobic effect [more info...]
Chain information for 247l #348
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 247l #348
---
CL — chloride ion
HED — 2-hydroxyethyl disulfide
1 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 11 C-terminal residues, 2 N-terminal residues, 69 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 247l chain A to query has RMSD 0.961 using 46 of 125 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 242l from http://files.rcsb.org/download/242l.cif
242l title:
The response of T4 lysozyme to large-to-small substitutions within the core
and its relation to the hydrophobic effect [more info...]
Chain information for 242l #349
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 242l #349
---
CL — chloride ion
HED — 2-hydroxyethyl disulfide
Deleted 11 C-terminal residues, 2 N-terminal residues, 87 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 242l chain A to query has RMSD 0.994 using 48 of 125 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 1l94 from http://files.rcsb.org/download/1l94.cif
1l94 title:
Similar hydrophobic replacements of leu 99 and phe 153 within the core of T4
lysozyme have different structural and thermodynamic consequences [more
info...]
Chain information for 1l94 #350
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYCV_BPT4 1-164
Non-standard residues in 1l94 #350
---
BME — β-mercaptoethanol
CL — chloride ion
Deleted 9 C-terminal residues, 2 N-terminal residues, 56 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1l94 chain A to query has RMSD 1.04 using 49 of 125 paired
residues within cutoff distance 2.0
1cu0 title:
T4 lysozyme mutant I78M [more info...]
Chain information for 1cu0 #351
---
Chain | Description | UniProt
A | LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 1cu0 #351
---
CL — chloride ion
HED — 2-hydroxyethyl disulfide
Deleted 9 C-terminal residues, 2 N-terminal residues, 44 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1cu0 chain A to query has RMSD 1.02 using 47 of 123 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 150l from http://files.rcsb.org/download/150l.cif
150l title:
Conservation of solvent-binding sites In 10 crystal forms of T4 lysozyme [more
info...]
Chain information for 150l #352
---
Chain | Description | UniProt
A B C D | T4 LYSOZYME | LYS_BPT4 1-164
150l mmCIF Assemblies
---
1| author_defined_assembly
2| author_and_software_defined_assembly
3| author_defined_assembly
4| author_and_software_defined_assembly
Deleted 3 extra chains, 9 C-terminal residues, 3 N-terminal residues, 155 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 150l chain B to query has RMSD 1.4 using 59 of 124 paired
residues within cutoff distance 2.0
5wf5 title:
Agonist bound human A2a adenosine receptor with D52N mutation at 2.60 A
resolution [more info...]
Chain information for 5wf5 #353
---
Chain | Description | UniProt
A | Human A2a adenosine receptor T4L chimera | AA2AR_HUMAN 2-208 222-316, ENLYS_BPT4 1002-1161
Non-standard residues in 5wf5 #353
---
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
UKA —
6-(2,2-diphenylethylamino)-9-[(2R,3R,4S,5S)-5-(ethylcarbamoyl)-3,4-dihydroxy-
oxolan-2-yl]-N-[2-[(1-pyridin-2-ylpiperidin-4-yl)carbamoylamino]ethyl]purine-2-carboxamide
17 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 94 C-terminal residues, 199 N-terminal residues, 4 non-polymer
residues more than 3.0 Angstroms away.
Alignment of 5wf5 chain A to query has RMSD 1.18 using 60 of 121 paired
residues within cutoff distance 2.0
1lyh title:
Dissection of helix capping In T4 lysozyme by structural and thermodynamic
analysis of six amino acid substitutions At THR 59 [more info...]
Chain information for 1lyh #354
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYCV_BPT4 1-164
Non-standard residues in 1lyh #354
---
BME — β-mercaptoethanol
CL — chloride ion
Deleted 9 C-terminal residues, 2 N-terminal residues, 57 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1lyh chain A to query has RMSD 0.99 using 48 of 125 paired
residues within cutoff distance 2.0
1l69 title:
Multiple stabilizing alanine replacements within α-helix 126-134 of T4
lysozyme have independent, additive effects on both structure and stability
[more info...]
Chain information for 1l69 #355
---
Chain | Description | UniProt
A | LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 1l69 #355
---
BME — β-mercaptoethanol
CL — chloride ion
Deleted 9 C-terminal residues, 2 N-terminal residues, 74 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1l69 chain A to query has RMSD 1.07 using 48 of 125 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 173l from http://files.rcsb.org/download/173l.cif
173l title:
Protein flexibility and adaptability seen In 25 crystal forms of T4 lysozyme
[more info...]
Chain information for 173l #356
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 173l #356
---
BME — β-mercaptoethanol
Deleted 9 C-terminal residues, 2 N-terminal residues, 58 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 173l chain A to query has RMSD 1.35 using 68 of 124 paired
residues within cutoff distance 2.0
141l title:
Role of backbone flexibility In the accommodation of variants that repack the
core of T4 lysozyme [more info...]
Chain information for 141l #357
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYCV_BPT4 1-164
Non-standard residues in 141l #357
---
BME — β-mercaptoethanol
CL — chloride ion
Deleted 9 C-terminal residues, 2 N-terminal residues, 54 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 141l chain A to query has RMSD 1.08 using 48 of 125 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 7mwz from http://files.rcsb.org/download/7mwz.cif
Fetching CCD 4UR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/4UR/4UR.cif
7mwz title:
Structure of drosophila STING in complex with 3'2'-cGAMP [more info...]
Chain information for 7mwz #358
---
Chain | Description
A B C D | STING
Non-standard residues in 7mwz #358
---
4UR — 3'2'-cGAMP
(2-amino-9-[(2S,5R,7R,8R,10R,12aR,14R,15R,15aS,16R)-7-(6-amino-9H-purin-9-yl)-2,10,15,16-tetrahydroxy-2,10-dioxidooctahydro-12H-5,8-methanofuro[3,2-l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecin-14-yl]-1,9-dihydro-6H-purin-6-one)
7mwz mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
10943 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 3 extra chains, 197 C-terminal residues, 3 N-terminal residues, 473
non-polymer residues more than 3.0 Angstroms away.
Alignment of 7mwz chain A to query has RMSD 1.11 using 58 of 124 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 6ffh from http://files.rcsb.org/download/6ffh.cif
Fetching CCD D7W from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/W/D7W/D7W.cif
Fetching CCD YCM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/YCM/YCM.cif
6ffh title:
Crystal Structure of mGluR5 in complex with Fenobam at 2.65 A [more info...]
Chain information for 6ffh #359
---
Chain | Description | UniProt
A | Metabotropic glutamate receptor 5,Endolysin | GRM5_HUMAN 569-678 1679-1836, ENLYS_BPT4 1002-1161
Non-standard residues in 6ffh #359
---
D7W — 1-(3-chlorophenyl)-3-(3-methyl-5-oxidanylidene-4~{H}-imidazol-2-yl)urea
MES — 2-(N-morpholino)-ethanesulfonic acid
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
3307 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 151 C-terminal residues, 112 N-terminal residues, 16 non-polymer
residues more than 3.0 Angstroms away.
Alignment of 6ffh chain A to query has RMSD 1.18 using 65 of 126 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 3sb7 from http://files.rcsb.org/download/3sb7.cif
3sb7 title:
Cu-mediated Trimer of T4 Lysozyme D61H/K65H/R76H/R80H by Synthetic
Symmetrization [more info...]
Chain information for 3sb7 #360
---
Chain | Description | UniProt
A B | Lysozyme | LYS_BPT4 1-162
Non-standard residues in 3sb7 #360
---
CU — copper (II) ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
3sb7 mmCIF Assemblies
---
1| author_defined_assembly
2| author_and_software_defined_assembly
2579 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 9 C-terminal residues, 3 N-terminal residues, 24 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 3sb7 chain A to query has RMSD 0.967 using 44 of 124 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 1cu3 from http://files.rcsb.org/download/1cu3.cif
1cu3 title:
T4 lysozyme mutant V87M [more info...]
Chain information for 1cu3 #361
---
Chain | Description | UniProt
A | LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 1cu3 #361
---
CL — chloride ion
HED — 2-hydroxyethyl disulfide
Deleted 9 C-terminal residues, 2 N-terminal residues, 62 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1cu3 chain A to query has RMSD 1.01 using 47 of 125 paired
residues within cutoff distance 2.0
3oe0 title:
Crystal structure of the CXCR4 chemokine receptor in complex with a cyclic
peptide antagonist CVX15 [more info...]
Chain information for 3oe0 #362
---
Chain | Description | UniProt
A | C-X-C chemokine receptor type 4, Lysozyme Chimera | CXCR4_HUMAN 2-228 231-319, LYS_BPT4 1002-1161
I | Polyphemusin analog, CXC chemokine receptor antagonist |
3oe0 mmCIF Assemblies
---
1| author_defined_assembly
3484 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 81 C-terminal residues, 197 N-terminal residues, 5
non-polymer residues more than 3.0 Angstroms away.
Alignment of 3oe0 chain A to query has RMSD 1.02 using 55 of 131 paired
residues within cutoff distance 2.0
250l title:
The response of T4 lysozyme to large-to-small substitutions within the core
and its relation to the hydrophobic effect [more info...]
Chain information for 250l #363
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 250l #363
---
CL — chloride ion
HED — 2-hydroxyethyl disulfide
Deleted 9 C-terminal residues, 2 N-terminal residues, 71 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 250l chain A to query has RMSD 0.938 using 46 of 125 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 209l from http://files.rcsb.org/download/209l.cif
209l title:
Protein structure plasticity exemplified by insertion and deletion mutants In
T4 lysozyme [more info...]
Chain information for 209l #364
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYS_BPT4 1-164
Deleted 8 C-terminal residues, 2 N-terminal residues, 11 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 209l chain A to query has RMSD 1.01 using 48 of 125 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 1p37 from http://files.rcsb.org/download/1p37.cif
1p37 title:
T4 lysozyme core repacking back-revertant L102M/CORE10 [more info...]
Chain information for 1p37 #365
---
Chain | Description | UniProt
A | LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 1p37 #365
---
CL — chloride ion
HED — 2-hydroxyethyl disulfide
K — potassium ion
14 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 11 C-terminal residues, 2 N-terminal residues, 118 non-polymer
residues more than 3.0 Angstroms away.
Alignment of 1p37 chain A to query has RMSD 0.93 using 45 of 127 paired
residues within cutoff distance 2.0
1l45 title:
Cumulative site-directed charge-change replacements In bacteriophage T4
lysozyme suggest that long-range electrostatic interactions contribute little
to protein stability [more info...]
Chain information for 1l45 #366
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYS_BPT4 1-164
Deleted 11 C-terminal residues, 2 N-terminal residues, 72 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1l45 chain A to query has RMSD 1.01 using 48 of 125 paired
residues within cutoff distance 2.0
1c6b title:
T4 lysozyme mutant C54T/C97A/L133A In the presence of 8 atm xenon [more
info...]
Chain information for 1c6b #367
---
Chain | Description | UniProt
A | PROTEIN (LYSOZYME) | LYS_BPT4 1-164
Non-standard residues in 1c6b #367
---
BME — β-mercaptoethanol
CL — chloride ion
XE — XENON
Deleted 9 C-terminal residues, 2 N-terminal residues, 60 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1c6b chain A to query has RMSD 1.03 using 48 of 125 paired
residues within cutoff distance 2.0
4rws title:
Crystal structure of CXCR4 and viral chemokine antagonist vMIP-II complex (PSI
Community Target) [more info...]
Chain information for 4rws #368
---
Chain | Description | UniProt
A | C-X-C chemokine receptor type 4/Endolysin chimeric protein | CXCR4_HUMAN 2-228 231-319, LYS_BPT4 1002-1161
C | Viral macrophage inflammatory protein 2 | VMI2_HHV8P 1-71
3953 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 84 C-terminal residues, 200 N-terminal residues.
Alignment of 4rws chain A to query has RMSD 1.05 using 54 of 126 paired
residues within cutoff distance 2.0
244l title:
The response of T4 lysozyme to large-to-small substitutions within the core
and its relation to the hydrophobic effect [more info...]
Chain information for 244l #369
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 244l #369
---
BME — β-mercaptoethanol
CL — chloride ion
HED — 2-hydroxyethyl disulfide
Deleted 9 C-terminal residues, 2 N-terminal residues, 61 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 244l chain A to query has RMSD 0.971 using 48 of 125 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 6kk7 from http://files.rcsb.org/download/6kk7.cif
Fetching CCD 97Y from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/97Y/97Y.cif
6kk7 title:
Structure of thermal-stabilised(M6) human GLP-1 receptor transmembrane domain
[more info...]
Chain information for 6kk7 #370
---
Chain | Description | UniProt
A B | Glucagon-like peptide 1 receptor,Endolysin,Glucagon-like peptide 1 receptor | GLP1R_HUMAN 128-257 261-431, ENLYS_BPT4 1001-1160
Non-standard residues in 6kk7 #370
---
97Y —
N-{4-[(R)-(3,3-dimethylcyclobutyl)({6-[4-(trifluoromethyl)-1H-imidazol-1-yl]pyridin-3-yl}amino)methyl]benzene-1-carbonyl}-beta-
alanine
6kk7 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
6590 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 162 C-terminal residues, 95 N-terminal residues, 2
non-polymer residues more than 3.0 Angstroms away.
Alignment of 6kk7 chain B to query has RMSD 0.929 using 46 of 142 paired
residues within cutoff distance 2.0
1l37 title:
Contributions of engineered surface salt bridges to the stability of T4
lysozyme determined by directed mutagenesis [more info...]
Chain information for 1l37 #371
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYS_BPT4 1-164
Deleted 11 C-terminal residues, 2 N-terminal residues, 72 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1l37 chain A to query has RMSD 0.955 using 46 of 125 paired
residues within cutoff distance 2.0
1d2w title:
N-terminal domain core methionine mutation [more info...]
Chain information for 1d2w #372
---
Chain | Description | UniProt
A | LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 1d2w #372
---
CL — chloride ion
HED — 2-hydroxyethyl disulfide
Deleted 9 C-terminal residues, 2 N-terminal residues, 63 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1d2w chain A to query has RMSD 0.959 using 47 of 127 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 1quo from http://files.rcsb.org/download/1quo.cif
1quo title:
L99A/E108V mutant of T4 lysozyme [more info...]
Chain information for 1quo #373
---
Chain | Description | UniProt
A | PROTEIN (LYSOZYME) | LYS_BPT4 1-162
Non-standard residues in 1quo #373
---
CL — chloride ion
HED — 2-hydroxyethyl disulfide
Deleted 9 C-terminal residues, 2 N-terminal residues, 50 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1quo chain A to query has RMSD 1.02 using 49 of 125 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 6xc1 from http://files.rcsb.org/download/6xc1.cif
6xc1 title:
Crystal structure of bacteriophage T4 spackle and lysozyme in orthorhombic
form [more info...]
Chain information for 6xc1 #374
---
Chain | Description | UniProt
A | Lysozyme | BP5_BPT4 174-342
C | Protein spackle | SPAC_BPT4 1-97
Non-standard residues in 6xc1 #374
---
EDO — 1,2-ethanediol (ethylene glycol)
IPA — isopropyl alcohol (2-propanol)
36 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
1923 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 10 C-terminal residues, 1 N-terminal residues, 74 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 6xc1 chain A to query has RMSD 1.36 using 51 of 127 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 5zty from http://files.rcsb.org/download/5zty.cif
Fetching CCD 9JU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/9JU/9JU.cif
Fetching CCD PG4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PG4/PG4.cif
5zty title:
Crystal structure of human G protein coupled receptor [more info...]
Chain information for 5zty #375
---
Chain | Description | UniProt
A | G protein coupled receptor,T4 lysozyme,G protein coupled receptor | CNR2_HUMAN 21-222 235-325, D9IEF7_BPT4 1001-1160
Non-standard residues in 5zty #375
---
9JU —
N-(adamantan-1-yl)-1-(5-hydroxypentyl)-4-methyl-5-phenyl-1H-pyrazole-3-carboxamide
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
PEG — di(hydroxyethyl)ether
PG4 — tetraethylene glycol
SO4 — sulfate ion
15 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
3508 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 93 C-terminal residues, 200 N-terminal residues, 48 non-polymer
residues more than 3.0 Angstroms away.
Alignment of 5zty chain A to query has RMSD 1.11 using 44 of 127 paired
residues within cutoff distance 2.0
1xju title:
Crystal structure of secreted inactive form of P1 phage endolysin Lyz [more
info...]
Chain information for 1xju #376
---
Chain | Description | UniProt
A B | Lysozyme | LYS_BPP1 29-185
Non-standard residues in 1xju #376
---
SO4 — sulfate ion
1xju mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| software_defined_assembly
Deleted 1 extra chains, 8 C-terminal residues, 35 N-terminal residues, 469
non-polymer residues more than 3.0 Angstroms away.
Alignment of 1xju chain A to query has RMSD 0.97 using 63 of 101 paired
residues within cutoff distance 2.0
1owz title:
T4 Lysozyme Cavity Mutant L99A/M102Q Bound With 4-FluoroPhenEthyl Alcohol
[more info...]
Chain information for 1owz #377
---
Chain | Description | UniProt
A | Lysozyme | LYS_BPT4 1-164
Non-standard residues in 1owz #377
---
4FA — 4-fluorophenethyl alcohol
BME — β-mercaptoethanol
CL — chloride ion
Deleted 9 C-terminal residues, 2 N-terminal residues, 19 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1owz chain A to query has RMSD 0.974 using 44 of 122 paired
residues within cutoff distance 2.0
7e40 title:
Mechanism of Phosphate Sensing and Signaling Revealed by Rice SPX1-PHR2
Complex Structure [more info...]
Chain information for 7e40 #378
---
Chain | Description | UniProt
A C | Protein PHOSPHATE STARVATION RESPONSE 2 | PHR2_ORYSJ 248-380
B D | SPX domain-containing protein 1,Endolysin | SPX1_ORYSJ 1-198, D9IEF7_BPT4 199-357
Non-standard residues in 7e40 #378
---
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)
7e40 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
7193 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 3 extra chains, 8 C-terminal residues, 137 N-terminal residues, 14
non-polymer residues more than 3.0 Angstroms away.
Alignment of 7e40 chain B to query has RMSD 1.27 using 61 of 158 paired
residues within cutoff distance 2.0
4n9n title:
Crystal Structure of Saccharomyces cerevisiae Upc2 Transcription Factor fused
with T4 Lysozyme [more info...]
Chain information for 4n9n #379
---
Chain | Description | UniProt
A B | Sterol uptake control protein 2, Lysozyme | UPC2_YEAST 598-714 726-878, LYS_BPT4 1002-1161
Deleted 1 extra chains, 163 C-terminal residues, 112 N-terminal residues, 24
non-polymer residues more than 3.0 Angstroms away.
Alignment of 4n9n chain A to query has RMSD 1.24 using 69 of 122 paired
residues within cutoff distance 2.0
4evx title:
Crystal structure of putative phage endolysin from S. enterica [more info...]
Chain information for 4evx #380
---
Chain | Description | UniProt
A B | Putative phage endolysin | Q8ZLC6_SALTY 5-107
4evx mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
3| software_defined_assembly
4| software_defined_assembly
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
1570 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 9 C-terminal residues, 2 N-terminal residues, 63 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 4evx chain A to query has RMSD 0.878 using 43 of 85 paired
residues within cutoff distance 2.0
3oe8 title:
Crystal structure of the CXCR4 chemokine receptor in complex with a small
molecule antagonist IT1t in P1 spacegroup [more info...]
Chain information for 3oe8 #381
---
Chain | Description | UniProt
A B C | C-X-C chemokine receptor type 4, Lysozyme Chimera | CXCR4_HUMAN 2-229 230-319, LYS_BPT4 1002-1161
Non-standard residues in 3oe8 #381
---
ITD — (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl
N,N'-dicyclohexylimidothiocarbamate
3oe8 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
3| software_defined_assembly
10292 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 2 extra chains, 82 C-terminal residues, 198 N-terminal residues, 3
non-polymer residues more than 3.0 Angstroms away.
Alignment of 3oe8 chain A to query has RMSD 1.02 using 48 of 124 paired
residues within cutoff distance 2.0
1xju title:
Crystal structure of secreted inactive form of P1 phage endolysin Lyz [more
info...]
Chain information for 1xju #382
---
Chain | Description | UniProt
A B | Lysozyme | LYS_BPP1 29-185
Non-standard residues in 1xju #382
---
SO4 — sulfate ion
1xju mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| software_defined_assembly
Deleted 1 extra chains, 8 C-terminal residues, 429 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 1xju chain B to query has RMSD 0.983 using 72 of 125 paired
residues within cutoff distance 2.0
1cvk title:
T4 lysozyme mutant L118A [more info...]
Chain information for 1cvk #383
---
Chain | Description | UniProt
A | LYSOZYME | LYS_BPT4 1-164
Non-standard residues in 1cvk #383
---
CL — chloride ion
HED — 2-hydroxyethyl disulfide
Deleted 9 C-terminal residues, 2 N-terminal residues, 56 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1cvk chain A to query has RMSD 0.993 using 48 of 125 paired
residues within cutoff distance 2.0
143l title:
Role of backbone flexibility In the accommodation of variants that repack the
core of T4 lysozyme [more info...]
Chain information for 143l #384
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYCV_BPT4 1-164
Non-standard residues in 143l #384
---
BME — β-mercaptoethanol
CL — chloride ion
Deleted 9 C-terminal residues, 2 N-terminal residues, 49 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 143l chain A to query has RMSD 1.05 using 50 of 125 paired
residues within cutoff distance 2.0
1l51 title:
Structural and thermodynamic analysis of the packing of two α-helices In
bacteriophage T4 lysozyme [more info...]
Chain information for 1l51 #385
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYS_BPT4 1-164
Deleted 11 C-terminal residues, 2 N-terminal residues, 69 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1l51 chain A to query has RMSD 1.03 using 46 of 127 paired
residues within cutoff distance 2.0
2nth title:
Structure of Spin-labeled T4 Lysozyme Mutant L118R1 [more info...]
Chain information for 2nth #386
---
Chain | Description | UniProt
A | Lysozyme | LYS_BPT4 1-164
Non-standard residues in 2nth #386
---
MTN — S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl]
methanesulfonothioate (MTSL)
Deleted 11 C-terminal residues, 2 N-terminal residues, 82 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 2nth chain A to query has RMSD 0.939 using 45 of 123 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 1ky1 from http://files.rcsb.org/download/1ky1.cif
1ky1 title:
Methionine core mutant of T4 lysozyme [more info...]
Chain information for 1ky1 #387
---
Chain | Description | UniProt
A | LYSOZYME | LYS_BPT4 1-162
Non-standard residues in 1ky1 #387
---
CL — chloride ion
HED — 2-hydroxyethyl disulfide
Deleted 9 C-terminal residues, 2 N-terminal residues, 53 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1ky1 chain A to query has RMSD 0.893 using 42 of 121 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 4k5y from http://files.rcsb.org/download/4k5y.cif
Fetching CCD PGW from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/W/PGW/PGW.cif
4k5y title:
Crystal structure of human corticotropin-releasing factor receptor 1 (CRF1R)
in complex with the antagonist CP-376395 [more info...]
Chain information for 4k5y #388
---
Chain | Description | UniProt
A B C | Corticotropin-releasing factor receptor 1, T4-Lysozyme chimeric construct | CRFR1_HUMAN 104-220 224-373, LYS_BPT4 1002-1161
Non-standard residues in 4k5y #388
---
1PE — pentaethylene glycol (PEG400)
1Q5 — 3,6-dimethyl-N-(pentan-3-yl)-2-(2,4,6-trimethylphenoxy)pyridin-4-amine
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
PGW —
(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl
(9Z)-octadec-9-enoate (1-Palmitoyl-2-Oleoyl-sn-
Glycero-3-[Phospho-(1-glycerol)]; PHOSPHATIDYLGLYCEROL)
SO4 — sulfate ion
4k5y mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
Deleted 2 extra chains, 149 C-terminal residues, 107 N-terminal residues, 20
non-polymer residues more than 3.0 Angstroms away.
Alignment of 4k5y chain A to query has RMSD 1.35 using 73 of 124 paired
residues within cutoff distance 2.0
4k5y title:
Crystal structure of human corticotropin-releasing factor receptor 1 (CRF1R)
in complex with the antagonist CP-376395 [more info...]
Chain information for 4k5y #389
---
Chain | Description | UniProt
A B C | Corticotropin-releasing factor receptor 1, T4-Lysozyme chimeric construct | CRFR1_HUMAN 104-220 224-373, LYS_BPT4 1002-1161
Non-standard residues in 4k5y #389
---
1PE — pentaethylene glycol (PEG400)
1Q5 — 3,6-dimethyl-N-(pentan-3-yl)-2-(2,4,6-trimethylphenoxy)pyridin-4-amine
OLA — oleic acid
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
PGW —
(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl
(9Z)-octadec-9-enoate (1-Palmitoyl-2-Oleoyl-sn-
Glycero-3-[Phospho-(1-glycerol)]; PHOSPHATIDYLGLYCEROL)
SO4 — sulfate ion
4k5y mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
Deleted 2 extra chains, 138 C-terminal residues, 107 N-terminal residues, 18
non-polymer residues more than 3.0 Angstroms away.
Alignment of 4k5y chain B to query has RMSD 1.3 using 73 of 126 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 140l from http://files.rcsb.org/download/140l.cif
140l title:
Role of backbone flexibility In the accommodation of variants that repack the
core of T4 lysozyme [more info...]
Chain information for 140l #390
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYCV_BPT4 1-164
Non-standard residues in 140l #390
---
BME — β-mercaptoethanol
CL — chloride ion
Deleted 9 C-terminal residues, 2 N-terminal residues, 50 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 140l chain A to query has RMSD 1.02 using 48 of 125 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 4ej4 from http://files.rcsb.org/download/4ej4.cif
Fetching CCD EJ4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/EJ4/EJ4.cif
4ej4 title:
Structure of the δ opioid receptor bound to naltrindole [more info...]
Chain information for 4ej4 #391
---
Chain | Description | UniProt
A | Delta-type opioid receptor, Lysozyme chimera | OPRD_MOUSE 36-244 251-342, LYS_BPT4 1002-1161
Non-standard residues in 4ej4 #391
---
EJ4 —
(4bS,8R,8aS,14bR)-7-(cyclopropylmethyl)-5,6,7,8,14,14b-hexahydro-4,8-methano[1]benzofuro[2,3-a]pyrido[4,3-b]carbazole-1,8a(9H)-diol
(Naltrindole)
Deleted 86 C-terminal residues, 205 N-terminal residues, 1 non-polymer
residues more than 3.0 Angstroms away.
Alignment of 4ej4 chain A to query has RMSD 1.06 using 51 of 125 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 1qtd from http://files.rcsb.org/download/1qtd.cif
1qtd title:
The introduction of strain and its effects on the structure and stability of
T4 lysozyme [more info...]
Chain information for 1qtd #392
---
Chain | Description | UniProt
A | LYSOZYME | LYS_BPT4 1-162
Non-standard residues in 1qtd #392
---
HED — 2-hydroxyethyl disulfide
Deleted 9 C-terminal residues, 2 N-terminal residues, 26 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1qtd chain A to query has RMSD 1.13 using 54 of 126 paired
residues within cutoff distance 2.0
4evx title:
Crystal structure of putative phage endolysin from S. enterica [more info...]
Chain information for 4evx #393
---
Chain | Description | UniProt
A B | Putative phage endolysin | Q8ZLC6_SALTY 5-107
4evx mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
3| software_defined_assembly
4| software_defined_assembly
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
1570 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 5 C-terminal residues, 64 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 4evx chain B to query has RMSD 0.853 using 41 of 89 paired
residues within cutoff distance 2.0
218l title:
Protein structure plasticity exemplified by insertion and deletion mutants In
T4 lysozyme [more info...]
Chain information for 218l #394
---
Chain | Description | UniProt
A | T4 LYSOZYME | LYS_BPT4 1-164
Deleted 9 C-terminal residues, 2 N-terminal residues, 39 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 218l chain A to query has RMSD 1.2 using 53 of 122 paired
residues within cutoff distance 2.0
5zkq title:
Crystal structure of the human platelet-activating factor receptor in complex
with ABT-491 [more info...]
Chain information for 5zkq #395
---
Chain | Description | UniProt
A B | Platelet-activating factor receptor,Endolysin,Endolysin,Platelet-activating factor receptor | PTAFR_HUMAN 2-218 224-316, ENLYS_BPT4 1001-1010 1017-1117
Non-standard residues in 5zkq #395
---
9EU —
4-ethynyl-3-{3-fluoro-4-[(2-methyl-1H-imidazo[4,5-c]pyridin-1-yl)methyl]benzene-1-carbonyl}-N,N-dimethyl-1H-indole-1-carboxamide
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)
SO4 — sulfate ion
ZN — zinc ion
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 85 C-terminal residues, 214 N-terminal residues, 16
non-polymer residues more than 3.0 Angstroms away.
Alignment of 5zkq chain B to query has RMSD 1.08 using 44 of 92 paired
residues within cutoff distance 2.0
3bkv title:
X-ray structure of the bacteriophage phiKZ lytic transglycosylase, gp144, in
complex with chitotetraose, (NAG)4 [more info...]
Chain information for 3bkv #396
---
Chain | Description | UniProt
A | lytic transglycosylase | Q8SD18_9CAUD 1-260
Non-standard residues in 3bkv #396
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
NI — nickel (II) ion
SO4 — sulfate ion
Deleted 4 C-terminal residues, 114 N-terminal residues, 6 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 3bkv chain A to query has RMSD 1.21 using 33 of 121 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 4dqj from http://files.rcsb.org/download/4dqj.cif
Fetching CCD AES from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/AES/AES.cif
4dqj title:
Structural Investigation of Bacteriophage Phi6 Lysin (in complex with
chitotetraose) [more info...]
Chain information for 4dqj #397
---
Chain | Description | UniProt
A B | Membrane protein Phi6 P5 | Q283U5_BPPH6 48-220
Non-standard residues in 4dqj #397
---
AES — 4-(2-aminoethyl)benzenesulfonyl fluoride (AEBSF)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
4dqj mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
62 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2723 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Deleted 1 extra chains, 4 C-terminal residues, 3 N-terminal residues, 306 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 4dqj chain A to query has RMSD 1.38 using 28 of 112 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 4eya from http://files.rcsb.org/download/4eya.cif
4eya title:
Crystal Structure of a Plectonemic RNA Supercoil [more info...]
Chain information for 4eya #398
---
Chain | Description | UniProt
A B C D E F G H | N utilization substance protein B homolog | NUSB_AQUAE 1-148
a b c d e f g h i j k l m n o p q r s t | RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3') |
Non-standard residues in 4eya #398
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
SO4 — sulfate ion
Deleted 27 extra chains, 10 C-terminal residues, 37 N-terminal residues, 16
non-polymer residues more than 3.0 Angstroms away.
Alignment of 4eya chain A to query has RMSD 0.768 using 23 of 80 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 7ao7 from http://files.rcsb.org/download/7ao7.cif
Fetching CCD HEM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/HEM/HEM.cif
Fetching CCD OC9 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/OC9/OC9.cif
7ao7 title:
Structure of CYP153A from Polaromonas sp. in complex with octan-1-ol [more
info...]
Chain information for 7ao7 #399
---
Chain | Description | UniProt
A B C D E F | Cytochrome P450 | Q11ZY2_POLSJ 1-418
Non-standard residues in 7ao7 #399
---
HEM — protoporphyrin IX containing Fe (HEME)
OC9 — octan-1-ol
7ao7 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
5| author_defined_assembly
6| author_defined_assembly
Deleted 5 extra chains, 98 C-terminal residues, 163 N-terminal residues, 358
non-polymer residues more than 3.0 Angstroms away.
Alignment of 7ao7 chain B to query has RMSD 1.03 using 14 of 95 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 4ye9 from http://files.rcsb.org/download/4ye9.cif
4ye9 title:
The crystal structure of the G45V mutant of human GlnRS [more info...]
Chain information for 4ye9 #400
---
Chain | Description | UniProt
A | Glutamine--tRNA ligase | SYQ_HUMAN 1-775
28 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 612 C-terminal residues, 15 N-terminal residues, 83 non-polymer
residues more than 3.0 Angstroms away.
Alignment of 4ye9 chain A to query has RMSD 0.814 using 13 of 71 paired
residues within cutoff distance 2.0
Fetching compressed mmCIF 7uqj from http://files.rcsb.org/download/7uqj.cif
Fetching CCD AGS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/AGS/AGS.cif
7uqj title:
Cryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 hexamer bound
to ATPgS and histone H3 tail in state II [more info...]
Chain information for 7uqj #401
---
Chain | Description | UniProt
A B C D E F | ATPase histone chaperone YTA7 | ATAD2_YEAST 1-1379
G | Histone H3 | H3_YEAST 1-25
Non-standard residues in 7uqj #401
---
ADP — adenosine-5'-diphosphate
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
Deleted 6 extra chains, 315 C-terminal residues, 181 N-terminal residues, 10
non-polymer residues more than 3.0 Angstroms away.
Alignment of 7uqj chain F to query has RMSD 1.29 using 25 of 79 paired
residues within cutoff distance 2.0
7uqj title:
Cryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 hexamer bound
to ATPgS and histone H3 tail in state II [more info...]
Chain information for 7uqj #402
---
Chain | Description | UniProt
A B C D E F | ATPase histone chaperone YTA7 | ATAD2_YEAST 1-1379
G | Histone H3 | H3_YEAST 1-25
Non-standard residues in 7uqj #402
---
ADP — adenosine-5'-diphosphate
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
Deleted 6 extra chains, 309 C-terminal residues, 187 N-terminal residues, 10
non-polymer residues more than 3.0 Angstroms away.
Alignment of 7uqj chain C to query has RMSD 1.3 using 27 of 70 paired residues
within cutoff distance 2.0
Fetching compressed mmCIF 3qz1 from http://files.rcsb.org/download/3qz1.cif
Fetching CCD 3QZ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/3QZ/3QZ.cif
3qz1 title:
Crystal Structure of Bovine Steroid of 21-hydroxylase (P450c21) [more info...]
Chain information for 3qz1 #403
---
Chain | Description | UniProt
A B C D | Steroid 21-hydroxylase | CP21A_BOVIN 1-496
Non-standard residues in 3qz1 #403
---
3QZ — (9beta)-17-hydroxypregn-4-ene-3,20-dione
HEM — protoporphyrin IX containing Fe (HEME)
3qz1 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
Deleted 3 extra chains, 176 C-terminal residues, 192 N-terminal residues, 108
non-polymer residues more than 3.0 Angstroms away.
Alignment of 3qz1 chain B to query has RMSD 1.04 using 15 of 67 paired
residues within cutoff distance 2.0
7uqj title:
Cryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 hexamer bound
to ATPgS and histone H3 tail in state II [more info...]
Chain information for 7uqj #404
---
Chain | Description | UniProt
A B C D E F | ATPase histone chaperone YTA7 | ATAD2_YEAST 1-1379
G | Histone H3 | H3_YEAST 1-25
Non-standard residues in 7uqj #404
---
ADP — adenosine-5'-diphosphate
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
Deleted 6 extra chains, 309 C-terminal residues, 184 N-terminal residues, 10
non-polymer residues more than 3.0 Angstroms away.
Alignment of 7uqj chain E to query has RMSD 1.25 using 25 of 74 paired
residues within cutoff distance 2.0
> select clear
> close
> open "/Users/gth_book/Documents/1_JOB_Files/Research_Proj_Prop/★
> Prop_2024_Enzybiotics ▲ 🌱/Structures_Analysis/Structure
> analysis/AbLys1_8APP_monom.pdb"
Chain information for AbLys1_8APP_monom.pdb #1
---
Chain | Description
A | No description available
> ui tool show "Similar Structures"
> foldseek /A
Found 404 similar structures to AbLys1_8APP_monom.pdb #1/A in pdb database
using foldseek, name fs1
> sequence search /A
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/similarstructures/gui.py", line 239, in _search
run(self.session, cmd)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/similarstructures/mmseqs2_search.py", line 39, in
mmseqs2_search
Mmseqs2WebQuery(session, chain, database=database,
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/similarstructures/mmseqs2_search.py", line 73, in __init__
chain_hits = add_chains_descrip_species(entity_hits)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/similarstructures/mmseqs2_search.py", line 206, in
add_chains_descrip_species
pdb_info = fetch_pdb_entity_info(set(entity_ids))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/similarstructures/mmseqs2_search.py", line 260, in
fetch_pdb_entity_info
f = urlopen(req)
^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 216, in urlopen
return opener.open(url, data, timeout)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 525, in open
response = meth(req, response)
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 634, in http_response
response = self.parent.error(
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 563, in error
return self._call_chain(*args)
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 496, in _call_chain
result = func(*args)
^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 643, in http_error_default
raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 415: Unsupported Media Type
urllib.error.HTTPError: HTTP Error 415: Unsupported Media Type
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 643, in http_error_default
raise HTTPError(req.full_url, code, msg, hdrs, fp)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Model Number: Z14Y000JEY/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 Performance and 2 Efficiency)
Memory: 16 GB
System Firmware Version: 18000.120.36
OS Loader Version: 18000.120.36
Software:
System Software Overview:
System Version: macOS 26.5 (25F71)
Kernel Version: Darwin 25.5.0
Time since boot: 14 hours, 30 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-CiliaBuilder: 1.1.0
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.26.1
ChimeraX-clix: 0.2.7
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DAQplugin: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NIHPresets: 1.2.8
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.5.4
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
coloredlogs: 15.0.1
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
flatbuffers: 25.12.19
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
humanfriendly: 10.0
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
joblib: 1.5.3
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
llvmlite: 0.46.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
MolecularDynamicsViewer: 1.6
mpmath: 1.3.0
mrcfile: 1.5.4
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numba: 0.64.0
numexpr: 2.14.1
numpy: 1.26.4
onnxruntime: 1.23.2
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
pandas: 3.0.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
protobuf: 6.33.5
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynndescent: 0.6.0
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scikit-learn: 1.8.0
scipy: 1.17.0
scipy: 1.14.0
Send2Trash: 2.1.0
SEQCROW: 1.9.7
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
sympy: 1.14.0
tables: 3.10.2
tcia_utils: 1.5.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
tqdm: 4.67.3
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
umap-learn: 0.5.11
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
Change History (2)
comment:1 by , 8 hours ago
| Component: | Unassigned → Sequence |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Parsing BlastProtein results failed: HTTP Error 415: Unsupported Media Type |
comment:2 by , 8 hours ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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