id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20389 Parsing BlastProtein results failed: HTTP Error 415: Unsupported Media Type chimerax-bug-report@… Zach Pearson "{{{ 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 }}} " defect assigned normal Sequence all ChimeraX