Ticket #7899: 1fvm-monomer-blue.pdb

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1HEADER PEPTIDE/ANTIBIOTIC 20-SEP-00 1FVM
2TITLE COMPLEX OF VANCOMYCIN WITH DI-ACETYL-LYS-D-ALA-D-ALA
3COMPND MOL_ID: 1;
4COMPND 2 MOLECULE: VANCOMYCIN;
5COMPND 3 CHAIN: A, B, C, D, E, F;
6COMPND 4 ENGINEERED: YES;
7COMPND 5 MOL_ID: 2;
8COMPND 6 MOLECULE: DI-ACETYL-LYS-D-ALA-D-ALA;
9COMPND 7 CHAIN: G, H, I, J, K, L;
10COMPND 8 ENGINEERED: YES
11SOURCE MOL_ID: 1;
12SOURCE 2 SYNTHETIC: YES;
13SOURCE 3 ORGANISM_SCIENTIFIC: AMYCOLATOPSIS ORIENTALIS;
14SOURCE 4 ORGANISM_TAXID: 31958;
15SOURCE 5 OTHER_DETAILS: SEQUENCE OCCURS IN NOCARDIA ORIENTALIS;
16SOURCE 6 MOL_ID: 2;
17SOURCE 7 SYNTHETIC: YES
18KEYWDS PEPTIDE-ANTIBIOTIC COMPLEX, GLYCOPEPTIDE, ANTIBIOTIC,
19KEYWDS 2 VANCOM CELL WALL PRECURSOR,
20KEYWDS 3 STRUCTURAL PROTEIN-ANTIBIOTIC COMPLEX
21EXPDTA X-RAY DIFFRACTION
22AUTHOR Y.NITANAI,K.KAKOI,K.AOKI
23REVDAT 5 27-JUL-11 1FVM 1 REMARK
24REVDAT 4 2 13-JUL-11 1FVM 1 VERSN
25REVDAT 3 3 24-FEB-09 1FVM 1 VERSN
26REVDAT 2 4 31-DEC-02 1FVM 1 REMARK
27REVDAT 1 5 01-NOV-00 1FVM 0
28JRNL AUTH Y.NITANAI,T.KIKUCHI,K.KAKOI,S.HANAMAKI,I.FUJISAWA,K.AOKI
29JRNL TITL CRYSTAL STRUCTURES OF THE COMPLEXES BETWEEN VANCOMYCIN AND
30JRNL TITL 2 CELL-WALL PRECURSOR ANALOGS.
31JRNL REF J.MOL.BIOL. V. 385 1422 2009
32JRNL REFN ISSN 0022-2836
33JRNL PMID 18976660
34JRNL DOI 10.1016/J.JMB.2008.10.026
35REMARK 2
36REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
37REMARK 3
38REMARK 3 REFINEMENT.
39REMARK 3 PROGRAM : X-PLOR 3.851
40REMARK 3 AUTHORS : BRUNGER
41REMARK 3
42REMARK 3 DATA USED IN REFINEMENT.
43REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
44REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00
45REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000
46REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000
47REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010
48REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.0
49REMARK 3 NUMBER OF REFLECTIONS : 7864
50REMARK 3
51REMARK 3 FIT TO DATA USED IN REFINEMENT.
52REMARK 3 CROSS-VALIDATION METHOD : NULL
53REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
54REMARK 3 R VALUE (WORKING SET) : 0.144
55REMARK 3 FREE R VALUE : NULL
56REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
57REMARK 3 FREE R VALUE TEST SET COUNT : NULL
58REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
59REMARK 3
60REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
61REMARK 3 TOTAL NUMBER OF BINS USED : 20
62REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80
63REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83
64REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.70
65REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 382
66REMARK 3 BIN R VALUE (WORKING SET) : 0.1480
67REMARK 3 BIN FREE R VALUE : NULL
68REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
69REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
70REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
71REMARK 3
72REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
73REMARK 3 PROTEIN ATOMS : 636
74REMARK 3 NUCLEIC ACID ATOMS : 0
75REMARK 3 HETEROGEN ATOMS : 126
76REMARK 3 SOLVENT ATOMS : 112
77REMARK 3
78REMARK 3 B VALUES.
79REMARK 3 FROM WILSON PLOT (A**2) : 6.80
80REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.50
81REMARK 3 OVERALL ANISOTROPIC B VALUE.
82REMARK 3 B11 (A**2) : NULL
83REMARK 3 B22 (A**2) : NULL
84REMARK 3 B33 (A**2) : NULL
85REMARK 3 B12 (A**2) : NULL
86REMARK 3 B13 (A**2) : NULL
87REMARK 3 B23 (A**2) : NULL
88REMARK 3
89REMARK 3 ESTIMATED COORDINATE ERROR.
90REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.13
91REMARK 3 ESD FROM SIGMAA (A) : 0.07
92REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
93REMARK 3
94REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
95REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
96REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
97REMARK 3
98REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
99REMARK 3 BOND LENGTHS (A) : 0.009
100REMARK 3 BOND ANGLES (DEGREES) : 1.05
101REMARK 3 DIHEDRAL ANGLES (DEGREES) : 0.76
102REMARK 3 IMPROPER ANGLES (DEGREES) : 1.34
103REMARK 3
104REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
105REMARK 3
106REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
107REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; 1.500
108REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; 2.000
109REMARK 3 SIDE-CHAIN BOND (A**2) : 1.350 ; 2.000
110REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.970 ; 2.500
111REMARK 3
112REMARK 3 NCS MODEL : NULL
113REMARK 3
114REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
115REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
116REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
117REMARK 3
118REMARK 3 PARAMETER FILE 1 : PARAM19X.SOL
119REMARK 3 PARAMETER FILE 2 : NULL
120REMARK 3 TOPOLOGY FILE 1 : TOPH19.SOL
121REMARK 3 TOPOLOGY FILE 2 : NULL
122REMARK 3
123REMARK 3 OTHER REFINEMENT REMARKS: NULL
124REMARK 4
125REMARK 4 1FVM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
126REMARK 100
127REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-OCT-00.
128REMARK 100 THE RCSB ID CODE IS RCSB011937.
129REMARK 200
130REMARK 200 EXPERIMENTAL DETAILS
131REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
132REMARK 200 DATE OF DATA COLLECTION : 24-JUN-00
133REMARK 200 TEMPERATURE (KELVIN) : 120
134REMARK 200 PH : 8.5
135REMARK 200 NUMBER OF CRYSTALS USED : 1
136REMARK 200
137REMARK 200 SYNCHROTRON (Y/N) : Y
138REMARK 200 RADIATION SOURCE : PHOTON FACTORY
139REMARK 200 BEAMLINE : BL-6A
140REMARK 200 X-RAY GENERATOR MODEL : NULL
141REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
142REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000
143REMARK 200 MONOCHROMATOR : FOCUSSING SILICON CRYSTAL
144REMARK 200 OPTICS : MIRRORS
145REMARK 200
146REMARK 200 DETECTOR TYPE : CCD
147REMARK 200 DETECTOR MANUFACTURER : ADSC QUAMTUM 4R
148REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
149REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA)
150REMARK 200
151REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8400
152REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
153REMARK 200 RESOLUTION RANGE LOW (A) : 25.500
154REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
155REMARK 200
156REMARK 200 OVERALL.
157REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
158REMARK 200 DATA REDUNDANCY : 6.800
159REMARK 200 R MERGE (I) : 0.04600
160REMARK 200 R SYM (I) : 0.04300
161REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7000
162REMARK 200
163REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
164REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
165REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90
166REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
167REMARK 200 DATA REDUNDANCY IN SHELL : 6.30
168REMARK 200 R MERGE FOR SHELL (I) : 0.07200
169REMARK 200 R SYM FOR SHELL (I) : 0.06600
170REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.500
171REMARK 200
172REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
173REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
174REMARK 200 SOFTWARE USED: AMORE
175REMARK 200 STARTING MODEL: PDB ENTRY 1AA5
176REMARK 200
177REMARK 200 REMARK: NULL
178REMARK 280
179REMARK 280 CRYSTAL
180REMARK 280 SOLVENT CONTENT, VS (%): 37.10
181REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95
182REMARK 280
183REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE PREPARED AT 293K FROM A
184REMARK 280 SOLUTION CONTAINING 6.6 MM VANCOMYCIN, 6.6 MM DI- ACETYL-LYS -D-
185REMARK 280 ALA-D-ALA, 3.3 % (V/V) ETHANOL, AND 0.66 M TRIS BUFFER PH 8.5, BY
186REMARK 280 EQUILIBRATING THE SOLUTION AGAINST A RESERVOIR SOLUTION
187REMARK 280 CONTAINING 10 % (V/V) ETHANOL AND 0.2 M TRIS BUFFER PH 8.5, VAPOR
188REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.0K
189REMARK 290
190REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
191REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
192REMARK 290
193REMARK 290 SYMOP SYMMETRY
194REMARK 290 NNNMMM OPERATOR
195REMARK 290 1555 X,Y,Z
196REMARK 290 2555 -X+1/2,-Y,Z+1/2
197REMARK 290 3555 -X,Y+1/2,-Z+1/2
198REMARK 290 4555 X+1/2,-Y+1/2,-Z
199REMARK 290
200REMARK 290 WHERE NNN -> OPERATOR NUMBER
201REMARK 290 MMM -> TRANSLATION VECTOR
202REMARK 290
203REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
204REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
205REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
206REMARK 290 RELATED MOLECULES.
207REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
208REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
209REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
210REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 17.81850
211REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
212REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.86400
213REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
214REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.21250
215REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.86400
216REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.81850
217REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.21250
218REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
219REMARK 290
220REMARK 290 REMARK: NULL
221REMARK 300
222REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5, 6
223REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
224REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
225REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
226REMARK 300 BURIED SURFACE AREA.
227REMARK 350
228REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
229REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
230REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
231REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
232REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
233REMARK 350
234REMARK 350 BIOMOLECULE: 1
235REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
236REMARK 350 SOFTWARE USED: PISA 1.18
237REMARK 350 TOTAL BURIED SURFACE AREA: 910 ANGSTROM**2
238REMARK 350 SURFACE AREA OF THE COMPLEX: 1540 ANGSTROM**2
239REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.9 KCAL/MOL
240REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, G
241REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
242REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
243REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
244REMARK 350
245REMARK 350 BIOMOLECULE: 2
246REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
247REMARK 350 SOFTWARE USED: PISA 1.18
248REMARK 350 TOTAL BURIED SURFACE AREA: 960 ANGSTROM**2
249REMARK 350 SURFACE AREA OF THE COMPLEX: 1480 ANGSTROM**2
250REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.6 KCAL/MOL
251REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, H
252REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
253REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
254REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
255REMARK 350
256REMARK 350 BIOMOLECULE: 3
257REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
258REMARK 350 SOFTWARE USED: PISA 1.18
259REMARK 350 TOTAL BURIED SURFACE AREA: 940 ANGSTROM**2
260REMARK 350 SURFACE AREA OF THE COMPLEX: 1540 ANGSTROM**2
261REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.6 KCAL/MOL
262REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, I
263REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
264REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
265REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
266REMARK 350
267REMARK 350 BIOMOLECULE: 4
268REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
269REMARK 350 SOFTWARE USED: PISA 1.18
270REMARK 350 TOTAL BURIED SURFACE AREA: 800 ANGSTROM**2
271REMARK 350 SURFACE AREA OF THE COMPLEX: 1630 ANGSTROM**2
272REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.7 KCAL/MOL
273REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, J
274REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
275REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
276REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
277REMARK 350
278REMARK 350 BIOMOLECULE: 5
279REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
280REMARK 350 SOFTWARE USED: PISA 1.18
281REMARK 350 TOTAL BURIED SURFACE AREA: 970 ANGSTROM**2
282REMARK 350 SURFACE AREA OF THE COMPLEX: 1430 ANGSTROM**2
283REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.2 KCAL/MOL
284REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, K
285REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
286REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
287REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
288REMARK 350
289REMARK 350 BIOMOLECULE: 6
290REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
291REMARK 350 SOFTWARE USED: PISA 1.18
292REMARK 350 TOTAL BURIED SURFACE AREA: 820 ANGSTROM**2
293REMARK 350 SURFACE AREA OF THE COMPLEX: 1640 ANGSTROM**2
294REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.7 KCAL/MOL
295REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, L
296REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
297REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
298REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
299REMARK 400
300REMARK 400 COMPOUND
301REMARK 400 VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS
302REMARK 400 A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS
303REMARK 400 FURTHER GLYCOSYLATED BY A DISACCHARIDE MADE OF D-GLUCOSE
304REMARK 400 AND VANCOSAMINE.
305REMARK 400 HERE, VANCOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE
306REMARK 400 SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) BGC AND RER.
307REMARK 400
308REMARK 400 GROUP: 1
309REMARK 400 NAME: VANCOMYCIN
310REMARK 400 CHAIN: A, B, C , D, E, F
311REMARK 400 COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 7
312REMARK 400 COMPONENT_2: SUGAR RESIDUES 8, 9
313REMARK 400 DESCRIPTION: VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE,
314REMARK 400 GLYCOSYLATED BY A DISACCHARIDE (RESIDUES 8
315REMARK 400 AND 9) ON RESIDUE 4.
316REMARK 500
317REMARK 500 GEOMETRY AND STEREOCHEMISTRY
318REMARK 500 SUBTOPIC: TORSION ANGLES
319REMARK 500
320REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
321REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
322REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
323REMARK 500
324REMARK 500 STANDARD TABLE:
325REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
326REMARK 500
327REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
328REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
329REMARK 500
330REMARK 500 M RES CSSEQI PSI PHI
331REMARK 500 ASN B 3 -58.41 -126.84
332REMARK 500 ASN D 3 -62.46 -102.93
333REMARK 500 ASN E 3 -71.29 -114.68
334REMARK 500 ASN F 3 -68.28 -105.07
335REMARK 500
336REMARK 500 REMARK: NULL
337REMARK 800
338REMARK 800 SITE
339REMARK 800 SITE_IDENTIFIER: AC1
340REMARK 800 EVIDENCE_CODE: SOFTWARE
341REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN A OF VANCOMYCIN
342REMARK 800
343REMARK 800 SITE_IDENTIFIER: AC2
344REMARK 800 EVIDENCE_CODE: SOFTWARE
345REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF VANCOMYCIN
346REMARK 800
347REMARK 800 SITE_IDENTIFIER: AC3
348REMARK 800 EVIDENCE_CODE: SOFTWARE
349REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF VANCOMYCIN
350REMARK 800
351REMARK 800 SITE_IDENTIFIER: AC4
352REMARK 800 EVIDENCE_CODE: SOFTWARE
353REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN D OF VANCOMYCIN
354REMARK 800
355REMARK 800 SITE_IDENTIFIER: AC5
356REMARK 800 EVIDENCE_CODE: SOFTWARE
357REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN E OF VANCOMYCIN
358REMARK 800
359REMARK 800 SITE_IDENTIFIER: AC6
360REMARK 800 EVIDENCE_CODE: SOFTWARE
361REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN F OF VANCOMYCIN
362REMARK 900
363REMARK 900 RELATED ENTRIES
364REMARK 900 RELATED ID: 1AA5 RELATED DB: PDB
365REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN
366REMARK 900 RELATED ID: 1C0Q RELATED DB: PDB
367REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH 2-ACETOXY-D-
368REMARK 900 PROPANOIC ACID
369REMARK 900 RELATED ID: 1C0R RELATED DB: PDB
370REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN WITH D-LACTIC ACID
371REMARK 900 RELATED ID: 1GAC RELATED DB: PDB
372REMARK 900 SOLUTION STRUCTURE OF A82846B COMPLEXED WITH ITS CELL WALL
373REMARK 900 PENTAPEPTIDE FRAGMENT
374REMARK 900 RELATED ID: 1GHG RELATED DB: PDB
375REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN AGLYCON
376REMARK 900 RELATED ID: 1PN3 RELATED DB: PDB
377REMARK 900 CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA
378REMARK 900 COMPLEXD WITH TDP AND DESVANCOSAMINYL VANCOMYCIN
379REMARK 900 RELATED ID: 1PNV RELATED DB: PDB
380REMARK 900 CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA
381REMARK 900 COMPLEXED WITH TDP AND VANCOMYCIN
382REMARK 900 RELATED ID: 1QD8 RELATED DB: PDB
383REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH N-ACETYL
384REMARK 900 GLYCIN
385REMARK 900 RELATED ID: 1RRV RELATED DB: PDB
386REMARK 900 CRYSTAL STRUCTURE OF TDP-VANCOSAMINYLTRANSFERASE GTFD
387REMARK 900 COMPLEXED WITH TDP AND DESVANCOSAMINYL VANCOMYCIN.
388REMARK 900 RELATED ID: 1SHO RELATED DB: PDB
389REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN
390DBREF 1FVM A 1 7 NOR NOR00681 NOR00681 1 7
391SEQRES 1 A 7 MLU OMZ ASN GHP GHP OMY 3FG
392HET MLU A 1 9
393HET OMZ A 2 14
394HET GHP A 4 11
395HET GHP A 5 11
396HET OMY A 6 14
397HET 3FG A 7 13
398HET BGC A 8 11
399HET RER A 9 10
400HETNAM MLU N-METHYLLEUCINE
401HETNAM OMZ (BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
402HETNAM GHP (2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
403HETNAM OMY (BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
404HETNAM 3FG (2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
405HETNAM DLS DI-ACETYL-LYSINE
406HETNAM DAL D-ALANINE
407HETNAM BGC BETA-D-GLUCOSE
408HETNAM RER (1R,3S,4S,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L-
409HETNAM 2 RER ARABINO-HEXOPYRANOSE
410HETSYN RER VANCOSAMINE
411FORMUL 1 MLU 6(C7 H15 N O2)
412FORMUL 1 OMZ 6(C9 H10 CL N O4)
413FORMUL 1 GHP 12(C8 H9 N O3)
414FORMUL 1 OMY 6(C9 H10 CL N O4)
415FORMUL 1 3FG 6(C8 H9 N O4)
416FORMUL 7 DLS 6(C10 H18 N2 O4)
417FORMUL 7 DAL 12(C3 H7 N O2)
418FORMUL 3 BGC 6(C6 H12 O6)
419FORMUL 3 RER 6(C7 H15 N O3)
420FORMUL 9 HOH *112(H2 O)
421LINK C MLU A 1 N OMZ A 2 1555 1555 1.350
422LINK C OMZ A 2 N ASN A 3 1555 1555 1.360
423LINK OH OMZ A 2 C5 GHP A 4 1555 1555 1.410
424LINK C ASN A 3 N GHP A 4 1555 1555 1.330
425LINK C GHP A 4 N GHP A 5 1555 1555 1.340
426LINK C3 GHP A 4 OCZ OMY A 6 1555 1555 1.400
427LINK O4 GHP A 4 C1 BGC A 8 1555 1555 1.390
428LINK C GHP A 5 N OMY A 6 1555 1555 1.350
429LINK C3 GHP A 5 CG1 3FG A 7 1555 1555 1.500
430LINK C OMY A 6 N 3FG A 7 1555 1555 1.340
431LINK O2 BGC A 8 C1 RER A 9 1555 1555 1.420
432LINK C OMY B 6 N 3FG B 7 1555 1555 1.330
433LINK C ASN E 3 N GHP E 4 1555 1555 1.320
434LINK C OMY E 6 N 3FG E 7 1555 1555 1.340
435CISPEP 1 GHP A 5 OMY A 6 0 1.25
436SITE 1 AC1 43 HOH A2001 HOH A2005 HOH A2006 HOH A2007
437SITE 2 AC1 43 HOH A2008 HOH A2009 HOH A2010 HOH A2011
438SITE 3 AC1 43 HOH A2012 HOH A2013 HOH A2014 HOH A2015
439SITE 4 AC1 43 HOH A2017 HOH A2018 HOH A2019 HOH A2020
440SITE 5 AC1 43 ASN B 3 GHP B 4 GHP B 5 OMY B 6
441SITE 6 AC1 43 BGC B 8 RER B 9 HOH B2004 HOH B2008
442SITE 7 AC1 43 HOH B2015 GHP C 5 MLU D 1 OMZ D 2
443SITE 8 AC1 43 ASN D 3 GHP D 5 3FG D 7 MLU E 1
444SITE 9 AC1 43 BGC E 8 HOH E2001 HOH E2020 MLU F 1
445SITE 10 AC1 43 BGC F 8 RER F 9 DLS G 1 DAL G 2
446SITE 11 AC1 43 DAL G 3 HOH G2002 DLS J 1
447SITE 1 AC2 37 OMZ A 2 ASN A 3 GHP A 4 GHP A 5
448SITE 2 AC2 37 OMY A 6 BGC A 8 RER A 9 HOH A2006
449SITE 3 AC2 37 HOH B2002 HOH B2003 HOH B2004 HOH B2007
450SITE 4 AC2 37 HOH B2008 HOH B2009 HOH B2010 HOH B2011
451SITE 5 AC2 37 HOH B2012 HOH B2013 HOH B2014 HOH B2015
452SITE 6 AC2 37 MLU C 1 MLU D 1 OMY D 6 3FG D 7
453SITE 7 AC2 37 RER D 9 HOH D2008 HOH D2009 HOH E2004
454SITE 8 AC2 37 MLU F 1 OMZ F 2 ASN F 3 GHP F 5
455SITE 9 AC2 37 3FG F 7 DLS H 1 DAL H 2 DAL H 3
456SITE 10 AC2 37 DLS J 1
457SITE 1 AC3 35 3FG A 7 HOH A2012 MLU B 1 HOH B2014
458SITE 2 AC3 35 HOH C2003 HOH C2004 HOH C2006 HOH C2008
459SITE 3 AC3 35 HOH C2009 HOH C2010 HOH C2011 HOH C2012
460SITE 4 AC3 35 HOH C2013 HOH C2014 OMZ D 2 ASN D 3
461SITE 5 AC3 35 GHP D 4 GHP D 5 OMY D 6 BGC D 8
462SITE 6 AC3 35 RER D 9 HOH D2005 HOH D2008 GHP E 5
463SITE 7 AC3 35 3FG E 7 HOH E2013 HOH E2019 HOH E2021
464SITE 8 AC3 35 3FG F 7 DLS H 1 DLS I 1 DAL I 2
465SITE 9 AC3 35 DAL I 3 DLS K 1 HOH K2001
466SITE 1 AC4 47 MLU A 1 ASN A 3 GHP A 4 GHP A 5
467SITE 2 AC4 47 3FG A 7 RER A 9 HOH A2012 GHP B 5
468SITE 3 AC4 47 OMY B 6 3FG B 7 RER B 9 HOH B2014
469SITE 4 AC4 47 OMZ C 2 ASN C 3 GHP C 4 GHP C 5
470SITE 5 AC4 47 OMY C 6 BGC C 8 HOH C2010 HOH C2012
471SITE 6 AC4 47 HOH D2001 HOH D2003 HOH D2004 HOH D2005
472SITE 7 AC4 47 HOH D2007 HOH D2008 HOH D2009 HOH D2010
473SITE 8 AC4 47 HOH D2011 HOH D2012 HOH D2013 MLU E 1
474SITE 9 AC4 47 OMZ E 2 ASN E 3 HOH E2003 HOH E2004
475SITE 10 AC4 47 MLU F 1 GHP F 5 OMY F 6 3FG F 7
476SITE 11 AC4 47 DAL G 2 HOH G2002 DLS J 1 DAL J 2
477SITE 12 AC4 47 DAL J 3 DLS L 1 DAL L 3
478SITE 1 AC5 40 MLU A 1 ASN A 3 RER A 9 HOH A2014
479SITE 2 AC5 40 HOH A2019 HOH B2010 MLU C 1 OMZ C 2
480SITE 3 AC5 40 RER C 9 HOH C2003 OMZ D 2 RER D 9
481SITE 4 AC5 40 HOH D2003 HOH E2001 HOH E2003 HOH E2004
482SITE 5 AC5 40 HOH E2006 HOH E2007 HOH E2008 HOH E2010
483SITE 6 AC5 40 HOH E2011 HOH E2012 HOH E2013 HOH E2015
484SITE 7 AC5 40 HOH E2017 HOH E2018 HOH E2019 HOH E2020
485SITE 8 AC5 40 HOH E2021 OMZ F 2 ASN F 3 GHP F 4
486SITE 9 AC5 40 GHP F 5 OMY F 6 BGC F 8 RER F 9
487SITE 10 AC5 40 DLS K 1 DAL K 2 DAL K 3 DLS L 1
488SITE 1 AC6 45 GHP A 5 3FG A 7 HOH A2009 HOH A2011
489SITE 2 AC6 45 MLU B 1 ASN B 3 GHP B 4 GHP B 5
490SITE 3 AC6 45 3FG B 7 HOH B2003 RER C 9 MLU D 1
491SITE 4 AC6 45 3FG D 7 RER D 9 HOH D2007 OMZ E 2
492SITE 5 AC6 45 ASN E 3 GHP E 4 GHP E 5 OMY E 6
493SITE 6 AC6 45 BGC E 8 RER E 9 HOH E2003 HOH E2017
494SITE 7 AC6 45 HOH F2001 HOH F2002 HOH F2003 HOH F2004
495SITE 8 AC6 45 HOH F2006 HOH F2007 HOH F2008 HOH F2009
496SITE 9 AC6 45 HOH F2010 HOH F2011 HOH F2012 HOH F2013
497SITE 10 AC6 45 HOH F2014 DLS G 1 DAL H 2 DLS J 1
498SITE 11 AC6 45 DAL J 3 DLS L 1 DAL L 2 DAL L 3
499SITE 12 AC6 45 HOH L2002
500CRYST1 35.637 36.425 65.728 90.00 90.00 90.00 P 21 21 21 24
501ORIGX1 1.000000 0.000000 0.000000 0.00000
502ORIGX2 0.000000 1.000000 0.000000 0.00000
503ORIGX3 0.000000 0.000000 1.000000 0.00000
504SCALE1 0.028061 0.000000 0.000000 0.00000
505SCALE2 0.000000 0.027454 0.000000 0.00000
506SCALE3 0.000000 0.000000 0.015214 0.00000
507HETATM 1 N MLU A 1 -3.746 5.901 32.054 1.00 10.57 N
508HETATM 2 CN MLU A 1 -3.475 7.242 32.631 1.00 8.78 C
509HETATM 3 CA MLU A 1 -2.685 5.427 31.112 1.00 9.32 C
510HETATM 4 C MLU A 1 -1.421 5.090 31.923 1.00 8.61 C
511HETATM 5 O MLU A 1 -1.513 4.700 33.076 1.00 9.05 O
512HETATM 6 CB MLU A 1 -3.118 4.163 30.379 1.00 9.04 C
513HETATM 7 CG MLU A 1 -4.319 4.218 29.421 1.00 9.77 C
514HETATM 8 CD1 MLU A 1 -4.059 5.124 28.278 1.00 10.82 C
515HETATM 9 CD2 MLU A 1 -4.576 2.810 28.898 1.00 9.78 C
516HETATM 10 N OMZ A 2 -0.235 5.218 31.294 1.00 6.08 N
517HETATM 11 CA OMZ A 2 0.978 4.864 32.003 1.00 5.01 C
518HETATM 12 C OMZ A 2 1.662 3.635 31.326 1.00 4.61 C
519HETATM 13 O OMZ A 2 2.575 3.062 31.906 1.00 5.14 O
520HETATM 14 CB OMZ A 2 2.027 6.038 32.141 1.00 4.44 C
521HETATM 15 OC OMZ A 2 1.433 7.179 32.740 1.00 4.06 O
522HETATM 16 CG OMZ A 2 2.569 6.364 30.789 1.00 3.67 C
523HETATM 17 CD1 OMZ A 2 3.801 5.827 30.401 1.00 4.01 C
524HETATM 18 CD2 OMZ A 2 1.864 7.179 29.891 1.00 3.84 C
525HETATM 19 CE1 OMZ A 2 4.303 6.094 29.141 1.00 4.09 C
526HETATM 20 CL OMZ A 2 5.831 5.416 28.686 1.00 8.11 CL
527HETATM 21 CE2 OMZ A 2 2.373 7.428 28.646 1.00 4.57 C
528HETATM 22 CZ OMZ A 2 3.591 6.878 28.268 1.00 4.83 C
529HETATM 23 OH OMZ A 2 4.054 7.131 26.998 1.00 5.04 O
530ATOM 24 N ASN A 3 1.188 3.256 30.112 1.00 4.73 N
531ATOM 25 CA ASN A 3 1.417 1.890 29.560 1.00 3.50 C
532ATOM 26 C ASN A 3 2.244 1.907 28.261 1.00 4.88 C
533ATOM 27 O ASN A 3 3.333 1.308 28.249 1.00 5.87 O
534ATOM 28 CB ASN A 3 0.102 1.184 29.350 1.00 3.14 C
535ATOM 29 CG ASN A 3 -0.781 1.101 30.578 1.00 4.06 C
536ATOM 30 OD1 ASN A 3 -0.314 1.300 31.722 1.00 4.73 O
537ATOM 31 ND2 ASN A 3 -2.053 0.803 30.327 1.00 2.84 N
538HETATM 32 N GHP A 4 1.738 2.541 27.211 1.00 5.12 N
539HETATM 33 CA GHP A 4 2.385 2.522 25.880 1.00 3.80 C
540HETATM 34 C GHP A 4 1.348 2.089 24.857 1.00 2.61 C
541HETATM 35 O GHP A 4 0.200 2.489 24.883 1.00 1.31 O
542HETATM 36 C1 GHP A 4 2.989 3.880 25.476 1.00 4.69 C
543HETATM 37 C2 GHP A 4 3.283 4.160 24.166 1.00 4.12 C
544HETATM 38 C3 GHP A 4 3.817 5.405 23.798 1.00 4.42 C
545HETATM 39 C4 GHP A 4 4.054 6.371 24.759 1.00 4.66 C
546HETATM 40 O4 GHP A 4 4.566 7.616 24.439 1.00 5.85 O
547HETATM 41 C5 GHP A 4 3.772 6.098 26.079 1.00 3.99 C
548HETATM 42 C6 GHP A 4 3.241 4.865 26.431 1.00 4.60 C
549HETATM 43 N GHP A 5 1.822 1.258 23.915 1.00 0.96 N
550HETATM 44 CA GHP A 5 1.166 1.059 22.652 1.00 1.29 C
551HETATM 45 C GHP A 5 2.246 0.795 21.569 1.00 2.40 C
552HETATM 46 O GHP A 5 3.327 0.339 21.938 1.00 4.26 O
553HETATM 47 C1 GHP A 5 0.162 -0.091 22.505 1.00 1.47 C
554HETATM 48 C2 GHP A 5 -1.092 0.174 22.007 1.00 1.74 C
555HETATM 49 C3 GHP A 5 -2.027 -0.838 21.722 1.00 1.60 C
556HETATM 50 C4 GHP A 5 -1.648 -2.172 21.974 1.00 3.17 C
557HETATM 51 O4 GHP A 5 -2.557 -3.167 21.701 1.00 1.84 O
558HETATM 52 C5 GHP A 5 -0.388 -2.443 22.487 1.00 2.35 C
559HETATM 53 C6 GHP A 5 0.520 -1.423 22.757 1.00 1.94 C
560HETATM 54 N OMY A 6 1.982 1.063 20.272 1.00 2.26 N
561HETATM 55 CA OMY A 6 0.799 1.608 19.695 1.00 2.41 C
562HETATM 56 OCZ OMY A 6 4.127 5.744 22.477 1.00 3.34 O
563HETATM 57 CE2 OMY A 6 4.110 4.269 20.620 1.00 3.22 C
564HETATM 58 CE1 OMY A 6 2.025 5.179 21.396 1.00 4.18 C
565HETATM 59 CZ OMY A 6 3.417 5.078 21.512 1.00 3.75 C
566HETATM 60 CG OMY A 6 2.023 3.674 19.561 1.00 2.22 C
567HETATM 61 CD2 OMY A 6 3.426 3.573 19.645 1.00 3.21 C
568HETATM 62 CD1 OMY A 6 1.333 4.501 20.447 1.00 2.93 C
569HETATM 63 CB OMY A 6 1.205 2.764 18.680 1.00 1.63 C
570HETATM 64 CL OMY A 6 1.100 6.199 22.491 1.00 5.78 CL
571HETATM 65 O OMY A 6 0.409 -0.463 18.522 1.00 2.26 O
572HETATM 66 C OMY A 6 -0.081 0.543 19.032 1.00 1.86 C
573HETATM 67 ODE OMY A 6 1.911 2.221 17.605 1.00 3.88 O
574HETATM 68 N 3FG A 7 -1.392 0.809 19.070 1.00 1.71 N
575HETATM 69 OD1 3FG A 7 -4.360 -0.595 23.349 1.00 3.94 O
576HETATM 70 CD1 3FG A 7 -4.452 -0.308 22.038 1.00 2.77 C
577HETATM 71 CG1 3FG A 7 -3.359 -0.414 21.175 1.00 2.34 C
578HETATM 72 CZ 3FG A 7 -5.715 0.107 21.567 1.00 2.86 C
579HETATM 73 CD2 3FG A 7 -5.894 0.415 20.242 1.00 2.08 C
580HETATM 74 OD2 3FG A 7 -7.059 0.824 19.723 1.00 4.33 O
581HETATM 75 CG2 3FG A 7 -4.804 0.303 19.348 1.00 1.77 C
582HETATM 76 CB 3FG A 7 -3.545 -0.110 19.807 1.00 2.44 C
583HETATM 77 CA 3FG A 7 -2.357 -0.246 18.836 1.00 2.54 C
584HETATM 78 C 3FG A 7 -2.843 -0.276 17.326 1.00 3.22 C
585HETATM 79 O 3FG A 7 -3.443 -1.350 17.022 1.00 3.30 O
586HETATM 80 OXT 3FG A 7 -2.621 0.668 16.610 1.00 2.62 O
587TER 81 3FG A 7
588HETATM 649 C2 BGC A 8 6.098 9.043 23.441 1.00 5.35 C
589HETATM 650 C3 BGC A 8 7.539 9.282 23.038 1.00 6.82 C
590HETATM 651 C4 BGC A 8 8.436 8.896 24.249 1.00 6.08 C
591HETATM 652 C5 BGC A 8 8.090 7.464 24.707 1.00 7.35 C
592HETATM 653 C6 BGC A 8 8.882 6.966 25.969 1.00 7.83 C
593HETATM 654 C1 BGC A 8 5.878 7.663 23.980 1.00 5.36 C
594HETATM 655 O2 BGC A 8 5.254 9.272 22.275 1.00 4.98 O
595HETATM 656 O3 BGC A 8 7.794 10.614 22.633 1.00 6.23 O
596HETATM 657 O4 BGC A 8 9.802 8.940 23.867 1.00 7.22 O
597HETATM 658 O5 BGC A 8 6.725 7.410 25.070 1.00 5.94 O
598HETATM 659 O6 BGC A 8 8.640 7.743 27.058 1.00 10.67 O
599HETATM 660 C1 RER A 9 4.555 10.505 22.211 1.00 4.96 C
600HETATM 661 C2 RER A 9 4.078 10.655 20.777 1.00 4.02 C
601HETATM 662 C3 RER A 9 2.866 9.782 20.445 1.00 5.16 C
602HETATM 663 N3 RER A 9 2.216 10.356 19.185 1.00 4.91 N
603HETATM 664 C3A RER A 9 3.232 8.374 20.073 1.00 3.64 C
604HETATM 665 C4 RER A 9 1.810 9.767 21.589 1.00 4.90 C
605HETATM 666 O4 RER A 9 1.224 11.137 21.530 1.00 5.02 O
606HETATM 667 C5 RER A 9 2.481 9.533 22.942 1.00 4.79 C
607HETATM 668 O5 RER A 9 3.529 10.479 23.167 1.00 3.94 O
608HETATM 669 C5A RER A 9 1.502 9.676 24.125 1.00 4.87 C
609END