PDB Short entry for 1FVM HEADER PEPTIDE/ANTIBIOTIC 20-SEP-00 1FVM TITLE COMPLEX OF VANCOMYCIN WITH DI-ACETYL-LYS-D-ALA-D-ALA COMPND MOL_ID: 1; COMPND 2 MOLECULE: VANCOMYCIN; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DI-ACETYL-LYS-D-ALA-D-ALA; COMPND 7 CHAIN: G, H, I, J, K, L; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: AMYCOLATOPSIS ORIENTALIS; SOURCE 4 ORGANISM_TAXID: 31958; SOURCE 5 OTHER_DETAILS: SEQUENCE OCCURS IN NOCARDIA ORIENTALIS; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES KEYWDS PEPTIDE-ANTIBIOTIC COMPLEX, GLYCOPEPTIDE, ANTIBIOTIC, VANCOMYCIN, KEYWDS 2 CELL WALL PRECURSOR, STRUCTURAL PROTEIN-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.NITANAI,K.KAKOI,K.AOKI REVDAT 8 15-NOV-23 1FVM 1 LINK REVDAT 7 25-OCT-23 1FVM 1 HETSYN REVDAT 6 29-JUL-20 1FVM 1 COMPND REMARK SEQRES HETNAM REVDAT 6 2 1 LINK SITE ATOM REVDAT 5 27-JUL-11 1FVM 1 REMARK REVDAT 4 13-JUL-11 1FVM 1 VERSN REVDAT 3 24-FEB-09 1FVM 1 VERSN REVDAT 2 31-DEC-02 1FVM 1 REMARK REVDAT 1 01-NOV-00 1FVM 0 JRNL AUTH Y.NITANAI,T.KIKUCHI,K.KAKOI,S.HANAMAKI,I.FUJISAWA,K.AOKI JRNL TITL CRYSTAL STRUCTURES OF THE COMPLEXES BETWEEN VANCOMYCIN AND JRNL TITL 2 CELL-WALL PRECURSOR ANALOGS. JRNL REF J.MOL.BIOL. V. 385 1422 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 18976660 JRNL DOI 10.1016/J.JMB.2008.10.026 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 7864 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 382 REMARK 3 BIN R VALUE (WORKING SET) : 0.1480 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 : 636 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 126 REMARK 3 SOLVENT ATOMS : 112 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.50 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) : 0.13 REMARK 3 ESD FROM SIGMAA (A) : 0.07 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.050 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 0.760 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.340 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.350 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.970 ; 2.500 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 : PARAM19X.SOL REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FVM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1000011937. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-00 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : FOCUSSING SILICON CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUAMTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8400 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : 0.04300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.07200 REMARK 200 R SYM FOR SHELL (I) : 0.06600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.500 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 1AA5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE PREPARED AT 293K FROM A REMARK 280 SOLUTION CONTAINING 6.6 MM VANCOMYCIN, 6.6 MM DI- ACETYL-LYS -D- REMARK 280 ALA-D-ALA, 3.3 % (V/V) ETHANOL, AND 0.66 M TRIS BUFFER PH 8.5, REMARK 280 BY EQUILIBRATING THE SOLUTION AGAINST A RESERVOIR SOLUTION REMARK 280 CONTAINING 10 % (V/V) ETHANOL AND 0.2 M TRIS BUFFER PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 17.81850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.86400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.21250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.86400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.81850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.21250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5, 6 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 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 1.18 REMARK 350 TOTAL BURIED SURFACE AREA: 910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, G, M 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 1.18 REMARK 350 TOTAL BURIED SURFACE AREA: 960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, H, N 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: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 1.18 REMARK 350 TOTAL BURIED SURFACE AREA: 940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, I, O 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: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 1.18 REMARK 350 TOTAL BURIED SURFACE AREA: 800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, J, P 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: 5 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 1.18 REMARK 350 TOTAL BURIED SURFACE AREA: 970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, K, Q 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: 6 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 1.18 REMARK 350 TOTAL BURIED SURFACE AREA: 820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, L, R 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 IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS REMARK 400 A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS REMARK 400 FURTHER GLYCOSYLATED BY A DISACCHARIDE MADE OF D-GLUCOSE REMARK 400 AND VANCOSAMINE. REMARK 400 HERE, VANCOMYCIN IS REPRESENTED BY GROUPING TOUGHER THE REMARK 400 SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) BGC AND RER. REMARK 400 REMARK 400 THE VANCOMYCIN IS GLYCOPEPTIDE, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: VANCOMYCIN REMARK 400 CHAIN: A, B, C, D, E, F, M, N, O, P, Q, R REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_2: RESIDUE BGC REMARK 400 COMPONENT_3: RESIDUE RER REMARK 400 DESCRIPTION: VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED REMARK 400 BY A DISACCHARIDE (RESIDUES 8 AND 9) ON RESIDUE 4. 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 ASN B 3 -58.41 -126.84 REMARK 500 ASN D 3 -62.46 -102.93 REMARK 500 ASN E 3 -71.29 -114.68 REMARK 500 ASN F 3 -68.28 -105.07 REMARK 500 REMARK 500 REMARK: NULL 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: 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: 1RRV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TDP-VANCOSAMINYLTRANSFERASE GTFD COMPLEXED REMARK 900 WITH TDP AND DESVANCOSAMINYL VANCOMYCIN. REMARK 900 RELATED ID: 1SHO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VANCOMYCIN DBREF 1FVM A 1 7 NOR NOR00681 NOR00681 1 7 DBREF 1FVM B 1 7 NOR NOR00681 NOR00681 1 7 DBREF 1FVM C 1 7 NOR NOR00681 NOR00681 1 7 DBREF 1FVM D 1 7 NOR NOR00681 NOR00681 1 7 DBREF 1FVM E 1 7 NOR NOR00681 NOR00681 1 7 DBREF 1FVM F 1 7 NOR NOR00681 NOR00681 1 7 DBREF 1FVM G 1 3 PDB 1FVM 1FVM 1 3 DBREF 1FVM H 1 3 PDB 1FVM 1FVM 1 3 DBREF 1FVM I 1 3 PDB 1FVM 1FVM 1 3 DBREF 1FVM J 1 3 PDB 1FVM 1FVM 1 3 DBREF 1FVM K 1 3 PDB 1FVM 1FVM 1 3 DBREF 1FVM L 1 3 PDB 1FVM 1FVM 1 3 SEQRES 1 A 7 MLU OMZ ASN GHP GHP OMY 3FG SEQRES 1 B 7 MLU OMZ ASN GHP GHP OMY 3FG SEQRES 1 C 7 MLU OMZ ASN GHP GHP OMY 3FG SEQRES 1 D 7 MLU OMZ ASN GHP GHP OMY 3FG SEQRES 1 E 7 MLU OMZ ASN GHP GHP OMY 3FG SEQRES 1 F 7 MLU OMZ ASN GHP GHP OMY 3FG SEQRES 1 G 3 DLS DAL DAL SEQRES 1 H 3 DLS DAL DAL SEQRES 1 I 3 DLS DAL DAL SEQRES 1 J 3 DLS DAL DAL SEQRES 1 K 3 DLS DAL DAL SEQRES 1 L 3 DLS DAL DAL HET MLU A 1 9 HET OMZ A 2 14 HET GHP A 4 11 HET GHP A 5 11 HET OMY A 6 14 HET 3FG A 7 13 HET MLU B 1 9 HET OMZ B 2 14 HET GHP B 4 11 HET GHP B 5 11 HET OMY B 6 14 HET 3FG B 7 13 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 MLU E 1 9 HET OMZ E 2 14 HET GHP E 4 11 HET GHP E 5 11 HET OMY E 6 14 HET 3FG E 7 13 HET MLU F 1 9 HET OMZ F 2 14 HET GHP F 4 11 HET GHP F 5 11 HET OMY F 6 14 HET 3FG F 7 13 HET DLS G 1 15 HET DAL G 2 5 HET DAL G 3 6 HET DLS H 1 15 HET DAL H 2 5 HET DAL H 3 6 HET DLS I 1 15 HET DAL I 2 5 HET DAL I 3 6 HET DLS J 1 15 HET DAL J 2 5 HET DAL J 3 6 HET DLS K 1 15 HET DAL K 2 5 HET DAL K 3 6 HET DLS L 1 15 HET DAL L 2 5 HET DAL L 3 6 HET BGC M 1 11 HET RER M 2 10 HET BGC N 1 11 HET RER N 2 10 HET BGC O 1 11 HET RER O 2 10 HET BGC P 1 11 HET RER P 2 10 HET BGC Q 1 11 HET RER Q 2 10 HET BGC R 1 11 HET RER R 2 10 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 DLS DI-ACETYL-LYSINE HETNAM DAL D-ALANINE HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM RER VANCOSAMINE HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN RER (1R,3S,4S,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L- HETSYN 2 RER ARABINO-HEXOPYRANOSE FORMUL 1 MLU 6(C7 H15 N O2) FORMUL 1 OMZ 6(C9 H10 CL N O4) FORMUL 1 GHP 12(C8 H9 N O3) FORMUL 1 OMY 6(C9 H10 CL N O4) FORMUL 1 3FG 6(C8 H9 N O4) FORMUL 7 DLS 6(C10 H18 N2 O4) FORMUL 7 DAL 12(C3 H7 N O2) FORMUL 13 BGC 6(C6 H12 O6) FORMUL 13 RER 6(C7 H15 N O3) FORMUL 19 HOH *112(H2 O) LINK C MLU A 1 N OMZ A 2 1555 1555 1.35 LINK C OMZ A 2 N ASN A 3 1555 1555 1.36 LINK OH OMZ A 2 C5 GHP A 4 1555 1555 1.41 LINK C ASN A 3 N GHP A 4 1555 1555 1.33 LINK C GHP A 4 N GHP A 5 1555 1555 1.34 LINK C3 GHP A 4 OCZ OMY A 6 1555 1555 1.40 LINK O4 GHP A 4 C1 BGC M 1 1555 1555 1.39 LINK C GHP A 5 N OMY A 6 1555 1555 1.35 LINK C3 GHP A 5 CG1 3FG A 7 1555 1555 1.50 LINK C OMY A 6 N 3FG A 7 1555 1555 1.34 LINK C MLU B 1 N OMZ B 2 1555 1555 1.35 LINK C OMZ B 2 N ASN B 3 1555 1555 1.35 LINK OH OMZ B 2 C5 GHP B 4 1555 1555 1.40 LINK C ASN B 3 N GHP B 4 1555 1555 1.31 LINK C GHP B 4 N GHP B 5 1555 1555 1.36 LINK C3 GHP B 4 OCZ OMY B 6 1555 1555 1.40 LINK O4 GHP B 4 C1 BGC N 1 1555 1555 1.41 LINK C GHP B 5 N OMY B 6 1555 1555 1.34 LINK C3 GHP B 5 CG1 3FG B 7 1555 1555 1.51 LINK C OMY B 6 N 3FG B 7 1555 1555 1.33 LINK C MLU C 1 N OMZ C 2 1555 1555 1.36 LINK C OMZ C 2 N ASN C 3 1555 1555 1.33 LINK OH OMZ C 2 C5 GHP C 4 1555 1555 1.41 LINK C ASN C 3 N GHP C 4 1555 1555 1.32 LINK C GHP C 4 N GHP C 5 1555 1555 1.35 LINK C3 GHP C 4 OCZ OMY C 6 1555 1555 1.41 LINK O4 GHP C 4 C1 BGC O 1 1555 1555 1.40 LINK C GHP C 5 N OMY C 6 1555 1555 1.34 LINK C3 GHP C 5 CG1 3FG C 7 1555 1555 1.49 LINK C OMY C 6 N 3FG C 7 1555 1555 1.34 LINK C MLU D 1 N OMZ D 2 1555 1555 1.35 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 1.32 LINK C GHP D 4 N GHP D 5 1555 1555 1.35 LINK C3 GHP D 4 OCZ OMY D 6 1555 1555 1.40 LINK O4 GHP D 4 C1 BGC P 1 1555 1555 1.41 LINK C GHP D 5 N OMY D 6 1555 1555 1.35 LINK C3 GHP D 5 CG1 3FG D 7 1555 1555 1.51 LINK C OMY D 6 N 3FG D 7 1555 1555 1.34 LINK C MLU E 1 N OMZ E 2 1555 1555 1.35 LINK C OMZ E 2 N ASN E 3 1555 1555 1.34 LINK OH OMZ E 2 C5 GHP E 4 1555 1555 1.41 LINK C ASN E 3 N GHP E 4 1555 1555 1.32 LINK C GHP E 4 N GHP E 5 1555 1555 1.35 LINK C3 GHP E 4 OCZ OMY E 6 1555 1555 1.40 LINK O4 GHP E 4 C1 BGC Q 1 1555 1555 1.39 LINK C GHP E 5 N OMY E 6 1555 1555 1.34 LINK C3 GHP E 5 CG1 3FG E 7 1555 1555 1.51 LINK C OMY E 6 N 3FG E 7 1555 1555 1.34 LINK C MLU F 1 N OMZ F 2 1555 1555 1.36 LINK C OMZ F 2 N ASN F 3 1555 1555 1.35 LINK OH OMZ F 2 C5 GHP F 4 1555 1555 1.41 LINK C ASN F 3 N GHP F 4 1555 1555 1.32 LINK C GHP F 4 N GHP F 5 1555 1555 1.35 LINK C3 GHP F 4 OCZ OMY F 6 1555 1555 1.40 LINK O4 GHP F 4 C1 BGC R 1 1555 1555 1.40 LINK C GHP F 5 N OMY F 6 1555 1555 1.35 LINK C3 GHP F 5 CG1 3FG F 7 1555 1555 1.50 LINK C OMY F 6 N 3FG F 7 1555 1555 1.36 LINK C DLS G 1 N DAL G 2 1555 1555 1.33 LINK C DAL G 2 N DAL G 3 1555 1555 1.33 LINK C DLS H 1 N DAL H 2 1555 1555 1.33 LINK C DAL H 2 N DAL H 3 1555 1555 1.33 LINK C DLS I 1 N DAL I 2 1555 1555 1.34 LINK C DAL I 2 N DAL I 3 1555 1555 1.34 LINK C DLS J 1 N DAL J 2 1555 1555 1.33 LINK C DAL J 2 N DAL J 3 1555 1555 1.34 LINK C DLS K 1 N DAL K 2 1555 1555 1.33 LINK C DAL K 2 N DAL K 3 1555 1555 1.33 LINK C DLS L 1 N DAL L 2 1555 1555 1.34 LINK C DAL L 2 N DAL L 3 1555 1555 1.34 LINK O2 BGC M 1 C1 RER M 2 1555 1555 1.42 LINK O2 BGC N 1 C1 RER N 2 1555 1555 1.42 LINK O2 BGC O 1 C1 RER O 2 1555 1555 1.42 LINK O2 BGC P 1 C1 RER P 2 1555 1555 1.42 LINK O2 BGC Q 1 C1 RER Q 2 1555 1555 1.42 LINK O2 BGC R 1 C1 RER R 2 1555 1555 1.42 CISPEP 1 GHP A 5 OMY A 6 0 1.25 CISPEP 2 GHP B 5 OMY B 6 0 1.30 CISPEP 3 GHP C 5 OMY C 6 0 1.08 CISPEP 4 GHP D 5 OMY D 6 0 1.10 CISPEP 5 GHP E 5 OMY E 6 0 0.01 CISPEP 6 GHP F 5 OMY F 6 0 1.33 CRYST1 35.637 36.425 65.728 90.00 90.00 90.00 P 21 21 21 24 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 0.028061 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027454 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015214 0.00000 HETATM 1 N MLU A 1 -3.746 5.901 32.054 1.00 10.57 N HETATM 2 CN MLU A 1 -3.475 7.242 32.631 1.00 8.78 C HETATM 3 CA MLU A 1 -2.685 5.427 31.112 1.00 9.32 C HETATM 4 C MLU A 1 -1.421 5.090 31.923 1.00 8.61 C HETATM 5 O MLU A 1 -1.513 4.700 33.076 1.00 9.05 O HETATM 6 CB MLU A 1 -3.118 4.163 30.379 1.00 9.04 C HETATM 7 CG MLU A 1 -4.319 4.218 29.421 1.00 9.77 C HETATM 8 CD1 MLU A 1 -4.059 5.124 28.278 1.00 10.82 C HETATM 9 CD2 MLU A 1 -4.576 2.810 28.898 1.00 9.78 C HETATM 10 N OMZ A 2 -0.235 5.218 31.294 1.00 6.08 N HETATM 11 CA OMZ A 2 0.978 4.864 32.003 1.00 5.01 C HETATM 12 C OMZ A 2 1.662 3.635 31.326 1.00 4.61 C HETATM 13 O OMZ A 2 2.575 3.062 31.906 1.00 5.14 O HETATM 14 CB OMZ A 2 2.027 6.038 32.141 1.00 4.44 C HETATM 15 OC OMZ A 2 1.433 7.179 32.740 1.00 4.06 O HETATM 16 CG OMZ A 2 2.569 6.364 30.789 1.00 3.67 C HETATM 17 CD1 OMZ A 2 3.801 5.827 30.401 1.00 4.01 C HETATM 18 CD2 OMZ A 2 1.864 7.179 29.891 1.00 3.84 C HETATM 19 CE1 OMZ A 2 4.303 6.094 29.141 1.00 4.09 C HETATM 20 CL OMZ A 2 5.831 5.416 28.686 1.00 8.11 CL HETATM 21 CE2 OMZ A 2 2.373 7.428 28.646 1.00 4.57 C HETATM 22 CZ OMZ A 2 3.591 6.878 28.268 1.00 4.83 C HETATM 23 OH OMZ A 2 4.054 7.131 26.998 1.00 5.04 O