HEADER TRANSFERASE/ANTIBIOTIC 09-DEC-03 1RRV TITLE X-RAY CRYSTAL STRUCTURE OF TDP-VANCOSAMINYLTRANSFERASE GTFD AS A TITLE 2 COMPLEX WITH TDP AND THE NATURAL SUBSTRATE, DESVANCOSAMINYL TITLE 3 VANCOMYCIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOSYLTRANSFERASE GTFD; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DESVANCOSAMINYL VANCOMYCIN; COMPND 7 CHAIN: C, D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AMYCOLATOPSIS ORIENTALIS; SOURCE 3 ORGANISM_TAXID: 31958; SOURCE 4 GENE: GTFD; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: AMYCOLATOPSIS ORIENTALIS; SOURCE 12 ORGANISM_TAXID: 31958 KEYWDS GT-B, GLYCOSYLTRANSFERASE, ROSSMANN FOLD, GLYCOPEPTIDE, VACOSAMYCIN, KEYWDS 2 ANTIBIOTIC, TRANSFERASE-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.M.MULICHAK,W.LU,H.C.LOSEY,C.T.WALSH,R.M.GARAVITO REVDAT 9 15-NOV-23 1RRV 1 LINK REVDAT 8 23-AUG-23 1RRV 1 HETSYN REVDAT 7 29-JUL-20 1RRV 1 COMPND REMARK SEQADV SEQRES REVDAT 7 2 1 HETNAM LINK SITE REVDAT 6 01-NOV-17 1RRV 1 REMARK REVDAT 5 11-OCT-17 1RRV 1 REMARK REVDAT 4 27-JUL-11 1RRV 1 REMARK REVDAT 3 13-JUL-11 1RRV 1 VERSN REVDAT 2 24-FEB-09 1RRV 1 VERSN REVDAT 1 18-MAY-04 1RRV 0 JRNL AUTH A.M.MULICHAK,W.LU,H.C.LOSEY,C.T.WALSH,R.M.GARAVITO JRNL TITL CRYSTAL STRUCTURE OF VANCOSAMINYLTRANSFERASE GTFD FROM THE JRNL TITL 2 VANCOMYCIN BIOSYNTHETIC PATHWAY: INTERACTIONS WITH ACCEPTOR JRNL TITL 3 AND NUCLEOTIDE LIGANDS JRNL REF BIOCHEMISTRY V. 43 5170 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15122882 JRNL DOI 10.1021/BI036130C REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 55329 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2668 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5975 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 92 REMARK 3 SOLVENT ATOMS : 500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.270 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RRV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000020995. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66022 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07400 REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1PN3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA,K PHOSPHATE, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 32.06000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: BIOLOGICAL ASSEMBLY IS A MONOMER. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 VANCOMYCIN DESVANCOSAMINYL IS A TRICYCLIC GLYCOPEPTIDE, A MEMBER REMARK 400 OF THE VANCOMYCIN FAMILY. THE SCAFFOLD IS A HEPTAPEPTIDE WITH REMARK 400 THE CONFIGURATION D-D-L-D-D-L-L. IT IS FURTHER GLYCOSYLATED REMARK 400 BY A D-GLUCOSE REMARK 400 HERE, DESVANCOSAMINYL ANCOMYCIN IS REPRESENTED BY GROUPING REMARK 400 TOGETHER THE SEQUENCE (SEQRES) AND THE LIGAND (HET) BGC. REMARK 400 REMARK 400 THE DESVANCOSAMINYL VANCOMYCIN IS GLYCOPEPTIDE, A MEMBER OF REMARK 400 ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: DESVANCOSAMINYL VANCOMYCIN REMARK 400 CHAIN: C, D REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_2: RESIDUE BGC REMARK 400 DESCRIPTION: DESVANCOSAMINYL VANCOMYCIN IS AN INTERMIDIATE IN REMARK 400 VANCOMYCIN BIOSYNTHESIS. IT IS TRICYCLIC REMARK 400 GLYCOPEPTIDE, GLYCOSYLATED BY D-GLUCOSE (RESIDUE 8) REMARK 400 ON RESIDUE 4. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLU A 402 REMARK 465 LYS A 403 REMARK 465 PRO A 404 REMARK 465 ALA A 405 REMARK 465 VAL A 406 REMARK 465 PRO A 407 REMARK 465 ALA A 408 REMARK 465 LEU A 409 REMARK 465 GLU A 410 REMARK 465 HIS A 411 REMARK 465 HIS A 412 REMARK 465 HIS A 413 REMARK 465 HIS A 414 REMARK 465 HIS A 415 REMARK 465 HIS A 416 REMARK 465 ARG B 401 REMARK 465 GLU B 402 REMARK 465 LYS B 403 REMARK 465 PRO B 404 REMARK 465 ALA B 405 REMARK 465 VAL B 406 REMARK 465 PRO B 407 REMARK 465 ALA B 408 REMARK 465 LEU B 409 REMARK 465 GLU B 410 REMARK 465 HIS B 411 REMARK 465 HIS B 412 REMARK 465 HIS B 413 REMARK 465 HIS B 414 REMARK 465 HIS B 415 REMARK 465 HIS B 416 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 41 CG CD OE1 OE2 REMARK 470 GLU A 71 CG CD OE1 OE2 REMARK 470 GLU A 93 CG CD OE1 OE2 REMARK 470 GLU A 228 CG CD OE1 OE2 REMARK 470 ARG A 250 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 257 CD CE NZ REMARK 470 ASP A 284 CG OD1 OD2 REMARK 470 ARG A 285 NE CZ NH1 NH2 REMARK 470 GLU A 358 CD OE1 OE2 REMARK 470 GLU A 371 CG CD OE1 OE2 REMARK 470 GLU A 377 CD OE1 OE2 REMARK 470 ARG A 401 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 25 CD CE NZ REMARK 470 GLN B 30 CG CD OE1 NE2 REMARK 470 GLU B 41 CG CD OE1 OE2 REMARK 470 GLU B 71 CG CD OE1 OE2 REMARK 470 GLN B 74 CD OE1 NE2 REMARK 470 GLU B 93 CG CD OE1 OE2 REMARK 470 ARG B 152 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 183 CG CD OE1 OE2 REMARK 470 GLU B 192 CG CD OE1 OE2 REMARK 470 GLU B 228 CG CD OE1 OE2 REMARK 470 ARG B 250 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 257 CD CE NZ REMARK 470 ASP B 284 CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 278 70.61 48.29 REMARK 500 ASP A 292 -152.42 -105.15 REMARK 500 THR A 332 -115.39 42.11 REMARK 500 THR B 145 105.13 -40.02 REMARK 500 ASP B 292 -155.74 -113.00 REMARK 500 ASN B 295 97.38 -61.82 REMARK 500 THR B 332 -122.80 40.48 REMARK 500 VAL B 383 55.39 -115.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 417 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 311 OG REMARK 620 2 THR A 332 OG1 123.2 REMARK 620 3 ASP A 333 OD1 112.2 72.8 REMARK 620 4 GOL A1006 O2 73.3 152.3 124.9 REMARK 620 5 GOL A1006 O3 86.6 134.0 63.1 62.6 REMARK 620 6 HOH A2122 O 148.3 83.9 90.2 75.5 84.0 REMARK 620 7 HOH A2266 O 76.7 67.9 136.7 98.4 158.0 102.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 417 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 311 OG REMARK 620 2 THR B 332 OG1 128.2 REMARK 620 3 ASP B 333 OD1 109.0 76.4 REMARK 620 4 GOL B1007 O3 80.2 134.3 59.4 REMARK 620 5 GOL B1007 O2 78.0 146.5 118.3 62.1 REMARK 620 6 HOH B2044 O 149.3 78.3 90.9 90.9 71.9 REMARK 620 7 HOH B2151 O 83.2 63.8 135.6 161.2 105.9 99.1 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AA5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN REMARK 900 RELATED ID: 1C0Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH 2-ACETOXY-D- REMARK 900 PROPANOIC ACID REMARK 900 RELATED ID: 1C0R RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN WITH D-LACTIC ACID REMARK 900 RELATED ID: 1FVM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH DI-ACETYL-LYS-D-ALA- REMARK 900 D-ALA REMARK 900 RELATED ID: 1GAC RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A82846B COMPLEXED WITH ITS CELL WALL REMARK 900 PENTAPEPTIDE FRAGMENT REMARK 900 RELATED ID: 1GHG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN AGLYCON REMARK 900 RELATED ID: 1PN3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA COMPLEXD REMARK 900 WITH TDP AND DESVANCOSAMINYL VANCOMYCIN REMARK 900 RELATED ID: 1PNV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA COMPLEXED REMARK 900 WITH TDP AND VANCOMYCIN REMARK 900 RELATED ID: 1QD8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH N-ACETYL GLYCIN REMARK 900 RELATED ID: 1SHO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN DBREF 1RRV A 1 408 UNP Q9AFC7 Q9AFC7_AMYOR 1 408 DBREF 1RRV A 409 416 PDB 1RRV 1RRV 409 416 DBREF 1RRV B 1 408 UNP Q9AFC7 Q9AFC7_AMYOR 1 408 DBREF 1RRV B 409 416 PDB 1RRV 1RRV 409 416 DBREF 1RRV C 1 7 NOR NOR00681 NOR00681 1 7 DBREF 1RRV D 1 7 NOR NOR00681 NOR00681 1 7 SEQADV 1RRV LEU A 195 UNP Q9AFC7 CYS 195 CLONING ARTIFACT SEQADV 1RRV LEU A 196 UNP Q9AFC7 TRP 196 CLONING ARTIFACT SEQADV 1RRV ALA A 197 UNP Q9AFC7 PRO 197 CLONING ARTIFACT SEQADV 1RRV LEU A 409 UNP Q9AFC7 CLONING ARTIFACT SEQADV 1RRV GLU A 410 UNP Q9AFC7 CLONING ARTIFACT SEQADV 1RRV HIS A 411 UNP Q9AFC7 EXPRESSION TAG SEQADV 1RRV HIS A 412 UNP Q9AFC7 EXPRESSION TAG SEQADV 1RRV HIS A 413 UNP Q9AFC7 EXPRESSION TAG SEQADV 1RRV HIS A 414 UNP Q9AFC7 EXPRESSION TAG SEQADV 1RRV HIS A 415 UNP Q9AFC7 EXPRESSION TAG SEQADV 1RRV HIS A 416 UNP Q9AFC7 EXPRESSION TAG SEQADV 1RRV LEU B 195 UNP Q9AFC7 CYS 195 CLONING ARTIFACT SEQADV 1RRV LEU B 196 UNP Q9AFC7 TRP 196 CLONING ARTIFACT SEQADV 1RRV ALA B 197 UNP Q9AFC7 PRO 197 CLONING ARTIFACT SEQADV 1RRV LEU B 409 UNP Q9AFC7 CLONING ARTIFACT SEQADV 1RRV GLU B 410 UNP Q9AFC7 CLONING ARTIFACT SEQADV 1RRV HIS B 411 UNP Q9AFC7 EXPRESSION TAG SEQADV 1RRV HIS B 412 UNP Q9AFC7 EXPRESSION TAG SEQADV 1RRV HIS B 413 UNP Q9AFC7 EXPRESSION TAG SEQADV 1RRV HIS B 414 UNP Q9AFC7 EXPRESSION TAG SEQADV 1RRV HIS B 415 UNP Q9AFC7 EXPRESSION TAG SEQADV 1RRV HIS B 416 UNP Q9AFC7 EXPRESSION TAG SEQRES 1 A 416 MET ARG VAL LEU LEU SER VAL CYS GLY THR ARG GLY ASP SEQRES 2 A 416 VAL GLU ILE GLY VAL ALA LEU ALA ASP ARG LEU LYS ALA SEQRES 3 A 416 LEU GLY VAL GLN THR ARG MET CYS ALA PRO PRO ALA ALA SEQRES 4 A 416 GLU GLU ARG LEU ALA GLU VAL GLY VAL PRO HIS VAL PRO SEQRES 5 A 416 VAL GLY LEU PRO GLN HIS MET MET LEU GLN GLU GLY MET SEQRES 6 A 416 PRO PRO PRO PRO PRO GLU GLU GLU GLN ARG LEU ALA ALA SEQRES 7 A 416 MET THR VAL GLU MET GLN PHE ASP ALA VAL PRO GLY ALA SEQRES 8 A 416 ALA GLU GLY CYS ALA ALA VAL VAL ALA VAL GLY ASP LEU SEQRES 9 A 416 ALA ALA ALA THR GLY VAL ARG SER VAL ALA GLU LYS LEU SEQRES 10 A 416 GLY LEU PRO PHE PHE TYR SER VAL PRO SER PRO VAL TYR SEQRES 11 A 416 LEU ALA SER PRO HIS LEU PRO PRO ALA TYR ASP GLU PRO SEQRES 12 A 416 THR THR PRO GLY VAL THR ASP ILE ARG VAL LEU TRP GLU SEQRES 13 A 416 GLU ARG ALA ALA ARG PHE ALA ASP ARG TYR GLY PRO THR SEQRES 14 A 416 LEU ASN ARG ARG ARG ALA GLU ILE GLY LEU PRO PRO VAL SEQRES 15 A 416 GLU ASP VAL PHE GLY TYR GLY HIS GLY GLU ARG PRO LEU SEQRES 16 A 416 LEU ALA ALA ASP PRO VAL LEU ALA PRO LEU GLN PRO ASP SEQRES 17 A 416 VAL ASP ALA VAL GLN THR GLY ALA TRP LEU LEU SER ASP SEQRES 18 A 416 GLU ARG PRO LEU PRO PRO GLU LEU GLU ALA PHE LEU ALA SEQRES 19 A 416 ALA GLY SER PRO PRO VAL HIS ILE GLY PHE GLY SER SER SEQRES 20 A 416 SER GLY ARG GLY ILE ALA ASP ALA ALA LYS VAL ALA VAL SEQRES 21 A 416 GLU ALA ILE ARG ALA GLN GLY ARG ARG VAL ILE LEU SER SEQRES 22 A 416 ARG GLY TRP THR GLU LEU VAL LEU PRO ASP ASP ARG ASP SEQRES 23 A 416 ASP CYS PHE ALA ILE ASP GLU VAL ASN PHE GLN ALA LEU SEQRES 24 A 416 PHE ARG ARG VAL ALA ALA VAL ILE HIS HIS GLY SER ALA SEQRES 25 A 416 GLY THR GLU HIS VAL ALA THR ARG ALA GLY VAL PRO GLN SEQRES 26 A 416 LEU VAL ILE PRO ARG ASN THR ASP GLN PRO TYR PHE ALA SEQRES 27 A 416 GLY ARG VAL ALA ALA LEU GLY ILE GLY VAL ALA HIS ASP SEQRES 28 A 416 GLY PRO THR PRO THR PHE GLU SER LEU SER ALA ALA LEU SEQRES 29 A 416 THR THR VAL LEU ALA PRO GLU THR ARG ALA ARG ALA GLU SEQRES 30 A 416 ALA VAL ALA GLY MET VAL LEU THR ASP GLY ALA ALA ALA SEQRES 31 A 416 ALA ALA ASP LEU VAL LEU ALA ALA VAL GLY ARG GLU LYS SEQRES 32 A 416 PRO ALA VAL PRO ALA LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 416 MET ARG VAL LEU LEU SER VAL CYS GLY THR ARG GLY ASP SEQRES 2 B 416 VAL GLU ILE GLY VAL ALA LEU ALA ASP ARG LEU LYS ALA SEQRES 3 B 416 LEU GLY VAL GLN THR ARG MET CYS ALA PRO PRO ALA ALA SEQRES 4 B 416 GLU GLU ARG LEU ALA GLU VAL GLY VAL PRO HIS VAL PRO SEQRES 5 B 416 VAL GLY LEU PRO GLN HIS MET MET LEU GLN GLU GLY MET SEQRES 6 B 416 PRO PRO PRO PRO PRO GLU GLU GLU GLN ARG LEU ALA ALA SEQRES 7 B 416 MET THR VAL GLU MET GLN PHE ASP ALA VAL PRO GLY ALA SEQRES 8 B 416 ALA GLU GLY CYS ALA ALA VAL VAL ALA VAL GLY ASP LEU SEQRES 9 B 416 ALA ALA ALA THR GLY VAL ARG SER VAL ALA GLU LYS LEU SEQRES 10 B 416 GLY LEU PRO PHE PHE TYR SER VAL PRO SER PRO VAL TYR SEQRES 11 B 416 LEU ALA SER PRO HIS LEU PRO PRO ALA TYR ASP GLU PRO SEQRES 12 B 416 THR THR PRO GLY VAL THR ASP ILE ARG VAL LEU TRP GLU SEQRES 13 B 416 GLU ARG ALA ALA ARG PHE ALA ASP ARG TYR GLY PRO THR SEQRES 14 B 416 LEU ASN ARG ARG ARG ALA GLU ILE GLY LEU PRO PRO VAL SEQRES 15 B 416 GLU ASP VAL PHE GLY TYR GLY HIS GLY GLU ARG PRO LEU SEQRES 16 B 416 LEU ALA ALA ASP PRO VAL LEU ALA PRO LEU GLN PRO ASP SEQRES 17 B 416 VAL ASP ALA VAL GLN THR GLY ALA TRP LEU LEU SER ASP SEQRES 18 B 416 GLU ARG PRO LEU PRO PRO GLU LEU GLU ALA PHE LEU ALA SEQRES 19 B 416 ALA GLY SER PRO PRO VAL HIS ILE GLY PHE GLY SER SER SEQRES 20 B 416 SER GLY ARG GLY ILE ALA ASP ALA ALA LYS VAL ALA VAL SEQRES 21 B 416 GLU ALA ILE ARG ALA GLN GLY ARG ARG VAL ILE LEU SER SEQRES 22 B 416 ARG GLY TRP THR GLU LEU VAL LEU PRO ASP ASP ARG ASP SEQRES 23 B 416 ASP CYS PHE ALA ILE ASP GLU VAL ASN PHE GLN ALA LEU SEQRES 24 B 416 PHE ARG ARG VAL ALA ALA VAL ILE HIS HIS GLY SER ALA SEQRES 25 B 416 GLY THR GLU HIS VAL ALA THR ARG ALA GLY VAL PRO GLN SEQRES 26 B 416 LEU VAL ILE PRO ARG ASN THR ASP GLN PRO TYR PHE ALA SEQRES 27 B 416 GLY ARG VAL ALA ALA LEU GLY ILE GLY VAL ALA HIS ASP SEQRES 28 B 416 GLY PRO THR PRO THR PHE GLU SER LEU SER ALA ALA LEU SEQRES 29 B 416 THR THR VAL LEU ALA PRO GLU THR ARG ALA ARG ALA GLU SEQRES 30 B 416 ALA VAL ALA GLY MET VAL LEU THR ASP GLY ALA ALA ALA SEQRES 31 B 416 ALA ALA ASP LEU VAL LEU ALA ALA VAL GLY ARG GLU LYS SEQRES 32 B 416 PRO ALA VAL PRO ALA LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 C 7 MLU OMZ ASN GHP GHP OMY 3FG SEQRES 1 D 7 MLU OMZ ASN GHP GHP OMY 3FG HET MLU C 1 9 HET OMZ C 2 14 HET GHP C 4 11 HET GHP C 5 11 HET OMY C 6 14 HET 3FG C 7 13 HET MLU D 1 9 HET OMZ D 2 14 HET GHP D 4 11 HET GHP D 5 11 HET OMY D 6 14 HET 3FG D 7 13 HET K A 417 1 HET TYD A1003 25 HET GOL A1005 6 HET GOL A1006 6 HET K B 417 1 HET TYD B1004 25 HET GOL B1007 6 HET BGC C 8 11 HET BGC D 8 11 HETNAM MLU N-METHYL-D-LEUCINE HETNAM OMZ (BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE HETNAM GHP (2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID HETNAM OMY (BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE HETNAM 3FG (2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID HETNAM K POTASSIUM ION HETNAM TYD THYMIDINE-5'-DIPHOSPHATE HETNAM GOL GLYCEROL HETNAM BGC BETA-D-GLUCOPYRANOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 3 MLU 2(C7 H15 N O2) FORMUL 3 OMZ 2(C9 H10 CL N O4) FORMUL 3 GHP 4(C8 H9 N O3) FORMUL 3 OMY 2(C9 H10 CL N O4) FORMUL 3 3FG 2(C8 H9 N O4) FORMUL 5 K 2(K 1+) FORMUL 6 TYD 2(C10 H16 N2 O11 P2) FORMUL 7 GOL 3(C3 H8 O3) FORMUL 12 BGC 2(C6 H12 O6) FORMUL 14 HOH *500(H2 O) HELIX 1 1 THR A 10 LEU A 27 1 18 HELIX 2 2 PRO A 36 ALA A 38 5 3 HELIX 3 3 ALA A 39 GLY A 47 1 9 HELIX 4 4 PRO A 56 MET A 60 5 5 HELIX 5 5 PRO A 69 ALA A 92 1 24 HELIX 6 6 ASP A 103 GLY A 118 1 16 HELIX 7 7 SER A 127 LEU A 131 5 5 HELIX 8 8 ASP A 150 ILE A 177 1 28 HELIX 9 9 ASP A 184 GLY A 189 1 6 HELIX 10 10 PRO A 226 ALA A 235 1 10 HELIX 11 11 GLY A 249 GLN A 266 1 18 HELIX 12 12 ASN A 295 PHE A 300 1 6 HELIX 13 13 ARG A 301 VAL A 303 5 3 HELIX 14 14 SER A 311 GLY A 322 1 12 HELIX 15 15 ASP A 333 LEU A 344 1 12 HELIX 16 16 THR A 356 LEU A 368 1 13 HELIX 17 17 ALA A 369 ALA A 380 1 12 HELIX 18 18 ASP A 386 ARG A 401 1 16 HELIX 19 19 THR B 10 LEU B 27 1 18 HELIX 20 20 PRO B 36 ALA B 38 5 3 HELIX 21 21 ALA B 39 GLY B 47 1 9 HELIX 22 22 PRO B 56 MET B 60 5 5 HELIX 23 23 PRO B 69 ALA B 92 1 24 HELIX 24 24 ASP B 103 LEU B 117 1 15 HELIX 25 25 SER B 127 LEU B 131 5 5 HELIX 26 26 ASP B 150 ILE B 177 1 28 HELIX 27 27 ASP B 184 GLY B 189 1 6 HELIX 28 28 PRO B 226 ALA B 235 1 10 HELIX 29 29 GLY B 249 GLN B 266 1 18 HELIX 30 30 ASN B 295 PHE B 300 1 6 HELIX 31 31 SER B 311 ALA B 321 1 11 HELIX 32 32 ASP B 333 GLY B 345 1 13 HELIX 33 33 THR B 356 LEU B 368 1 13 HELIX 34 34 ALA B 369 GLY B 381 1 13 HELIX 35 35 ASP B 386 GLY B 400 1 15 SHEET 1 AA 6 HIS A 50 PRO A 52 0 SHEET 2 AA 6 GLN A 30 ALA A 35 1 O MET A 33 N VAL A 51 SHEET 3 AA 6 ARG A 2 CYS A 8 1 O VAL A 3 N ARG A 32 SHEET 4 AA 6 ALA A 97 GLY A 102 1 O ALA A 97 N LEU A 4 SHEET 5 AA 6 PHE A 121 VAL A 125 1 O PHE A 122 N ALA A 100 SHEET 6 AA 6 LEU A 195 LEU A 196 1 O LEU A 195 N VAL A 125 SHEET 1 AB 6 CYS A 288 ILE A 291 0 SHEET 2 AB 6 VAL A 270 SER A 273 1 O VAL A 270 N PHE A 289 SHEET 3 AB 6 VAL A 240 ILE A 242 1 O VAL A 240 N ILE A 271 SHEET 4 AB 6 ALA A 305 HIS A 308 1 O ALA A 305 N HIS A 241 SHEET 5 AB 6 GLN A 325 VAL A 327 1 O LEU A 326 N HIS A 308 SHEET 6 AB 6 GLY A 347 ALA A 349 1 O VAL A 348 N VAL A 327 SHEET 1 BA 6 HIS B 50 PRO B 52 0 SHEET 2 BA 6 GLN B 30 ALA B 35 1 O MET B 33 N VAL B 51 SHEET 3 BA 6 ARG B 2 CYS B 8 1 O VAL B 3 N ARG B 32 SHEET 4 BA 6 ALA B 97 GLY B 102 1 O ALA B 97 N LEU B 4 SHEET 5 BA 6 PHE B 121 VAL B 125 1 O PHE B 122 N ALA B 100 SHEET 6 BA 6 LEU B 195 LEU B 196 1 O LEU B 195 N VAL B 125 SHEET 1 BB 6 CYS B 288 ILE B 291 0 SHEET 2 BB 6 VAL B 270 SER B 273 1 O VAL B 270 N PHE B 289 SHEET 3 BB 6 VAL B 240 GLY B 243 1 O VAL B 240 N ILE B 271 SHEET 4 BB 6 ALA B 305 HIS B 308 1 O ALA B 305 N HIS B 241 SHEET 5 BB 6 GLN B 325 VAL B 327 1 O LEU B 326 N HIS B 308 SHEET 6 BB 6 GLY B 347 ALA B 349 1 O VAL B 348 N VAL B 327 LINK C MLU C 1 N OMZ C 2 1555 1555 1.36 LINK C OMZ C 2 N ASN C 3 1555 1555 1.36 LINK OH OMZ C 2 C5 GHP C 4 1555 1555 1.41 LINK C ASN C 3 N GHP C 4 1555 1555 1.31 LINK C GHP C 4 N GHP C 5 1555 1555 1.36 LINK C3 GHP C 4 OCZ OMY C 6 1555 1555 1.41 LINK O4 GHP C 4 C1 BGC C 8 1555 1555 1.42 LINK C GHP C 5 N OMY C 6 1555 1555 1.35 LINK C3 GHP C 5 CG1 3FG C 7 1555 1555 1.51 LINK C OMY C 6 N 3FG C 7 1555 1555 1.34 LINK C MLU D 1 N OMZ D 2 1555 1555 1.37 LINK C OMZ D 2 N ASN D 3 1555 1555 1.35 LINK OH OMZ D 2 C5 GHP D 4 1555 1555 1.41 LINK C ASN D 3 N GHP D 4 1555 1555 1.31 LINK C GHP D 4 N GHP D 5 1555 1555 1.36 LINK C3 GHP D 4 OCZ OMY D 6 1555 1555 1.42 LINK O4 GHP D 4 C1 BGC D 8 1555 1555 1.43 LINK C GHP D 5 N OMY D 6 1555 1555 1.36 LINK C3 GHP D 5 CG1 3FG D 7 1555 1555 1.53 LINK C OMY D 6 N 3FG D 7 1555 1555 1.35 LINK OG SER A 311 K K A 417 1555 1555 2.97 LINK OG1 THR A 332 K K A 417 1555 1555 2.83 LINK OD1 ASP A 333 K K A 417 1555 1555 2.71 LINK K K A 417 O2 GOL A1006 1555 1555 2.86 LINK K K A 417 O3 GOL A1006 1555 1555 2.71 LINK K K A 417 O HOH A2122 1555 1555 2.86 LINK K K A 417 O HOH A2266 1555 1555 2.95 LINK OG SER B 311 K K B 417 1555 1555 3.20 LINK OG1 THR B 332 K K B 417 1555 1555 2.88 LINK OD1 ASP B 333 K K B 417 1555 1555 2.91 LINK K K B 417 O3 GOL B1007 1555 1555 2.64 LINK K K B 417 O2 GOL B1007 1555 1555 2.88 LINK K K B 417 O HOH B2044 1555 1555 2.70 LINK K K B 417 O HOH B2151 1555 1555 2.95 CISPEP 1 GHP C 5 OMY C 6 0 2.89 CISPEP 2 GHP D 5 OMY D 6 0 3.02 CRYST1 50.670 64.120 144.080 90.00 91.73 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.019736 0.000000 0.000596 0.00000 SCALE2 0.000000 0.015596 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006944 0.00000