HEADER ISOMERASE 10-JUL-12 4B1F TITLE DESIGN OF INHIBITORS OF HELICOBACTER PYLORI GLUTAMATE RACEMASE AS TITLE 2 SELECTIVE ANTIBACTERIAL AGENTS: INCORPORATION OF IMIDAZOLES ONTO A TITLE 3 CORE PYRAZOLOPYRIMIDINEDIONE SCAFFOLD TO IMPROVE BIOAVAILABILTY COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE RACEMASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 5.1.1.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 210; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ISOMERASE, IMPROVED BIOAVAILABILITY EXPDTA X-RAY DIFFRACTION AUTHOR G.S.BASARAB,P.HILL,C.J.EYERMANN,M.GOWRAVARAM,H.KACK,E.OSIMONI REVDAT 4 08-MAY-24 4B1F 1 REMARK REVDAT 3 02-MAY-18 4B1F 1 AUTHOR REVDAT 2 10-OCT-12 4B1F 1 JRNL REVDAT 1 18-JUL-12 4B1F 0 JRNL AUTH G.S.BASARAB,P.HILL,C.J.EYERMANN,M.GOWRAVARAM,H.KACK, JRNL AUTH 2 E.OSIMONI JRNL TITL DESIGN OF INHIBITORS OF HELICOBACTER PYLORI GLUTAMATE JRNL TITL 2 RACEMASE AS SELECTIVE ANTIBACTERIAL AGENTS: INCORPORATION OF JRNL TITL 3 IMIDAZOLES ONTO A CORE PYRAZOLOPYRIMIDINEDIONE SCAFFOLD TO JRNL TITL 4 IMPROVE BIOAVAILABILTY. JRNL REF BIOORG.MED.CHEM.LETT. V. 22 5600 2012 JRNL REFN ISSN 0960-894X JRNL PMID 22877632 JRNL DOI 10.1016/J.BMCL.2012.07.004 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0027 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 29091 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 + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1574 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.11 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1884 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.28 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 94 REMARK 3 BIN FREE R VALUE : 0.3470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4024 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 221 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : -0.38000 REMARK 3 B33 (A**2) : 0.52000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.240 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.197 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.129 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.882 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4212 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4060 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5726 ; 1.830 ; 2.007 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9386 ; 0.851 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 508 ; 6.458 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 166 ;40.802 ;25.060 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 724 ;14.471 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;20.107 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 646 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4668 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 878 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 255 REMARK 3 ORIGIN FOR THE GROUP (A): 27.4000 -12.7430 -13.4560 REMARK 3 T TENSOR REMARK 3 T11: 0.0633 T22: 0.0183 REMARK 3 T33: 0.0800 T12: 0.0088 REMARK 3 T13: -0.0063 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 1.2270 L22: 0.6284 REMARK 3 L33: 0.8503 L12: -0.8214 REMARK 3 L13: -0.0470 L23: -0.2260 REMARK 3 S TENSOR REMARK 3 S11: -0.1699 S12: 0.0634 S13: 0.0623 REMARK 3 S21: 0.0823 S22: -0.0445 S23: -0.1048 REMARK 3 S31: 0.0989 S32: -0.0008 S33: 0.2144 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 255 REMARK 3 ORIGIN FOR THE GROUP (A): 3.6800 11.5880 -12.3270 REMARK 3 T TENSOR REMARK 3 T11: 0.0549 T22: 0.0559 REMARK 3 T33: 0.0745 T12: 0.0311 REMARK 3 T13: 0.0125 T23: 0.0232 REMARK 3 L TENSOR REMARK 3 L11: 0.3311 L22: 0.3822 REMARK 3 L33: 1.2816 L12: -0.1694 REMARK 3 L13: 0.1435 L23: 0.3317 REMARK 3 S TENSOR REMARK 3 S11: 0.0534 S12: 0.0353 S13: -0.0090 REMARK 3 S21: 0.0281 S22: 0.0084 S23: 0.0246 REMARK 3 S31: -0.0441 S32: -0.0983 S33: -0.0618 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 4B1F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1290053284. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.064 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29091 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 6.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 30.96650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.46750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.98700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.46750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.96650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.98700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 26 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 GLU A 150 OE1 - CD - OE2 ANGL. DEV. = 7.3 DEGREES REMARK 500 ASP B 26 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ALA A 200 44.67 -87.08 REMARK 500 ASN A 226 44.65 78.30 REMARK 500 ASP A 241 54.64 35.77 REMARK 500 LYS A 254 23.92 82.28 REMARK 500 ASN B 123 28.61 49.27 REMARK 500 ASN B 226 43.38 -89.36 REMARK 500 ASN B 227 49.45 -153.35 REMARK 500 LYS B 254 40.26 74.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 239 GLY A 240 149.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGL B 1256 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KRH A 1256 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KRH B 1257 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGL A 1257 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JFX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GLUTAMATE RACEMASE IN REMARK 900 COMPLEX WITH D-GLUTAMATE REMARK 900 RELATED ID: 2JFY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GLUTAMATE RACEMASE IN REMARK 900 COMPLEX WITH D-GLUTAMATE REMARK 900 RELATED ID: 2JFZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GLUTAMATE RACEMASE IN REMARK 900 COMPLEX WITH D-GLUTAMATE AND AN INHIBITOR REMARK 900 RELATED ID: 2W4I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GLUTAMATE RACEMASE IN REMARK 900 COMPLEX WITH D-GLUTAMATE AND AN INHIBITOR DBREF 4B1F A 1 255 UNP Q9ZLT0 MURI_HELPJ 1 255 DBREF 4B1F B 1 255 UNP Q9ZLT0 MURI_HELPJ 1 255 SEQRES 1 A 255 MET LYS ILE GLY VAL PHE ASP SER GLY VAL GLY GLY PHE SEQRES 2 A 255 SER VAL LEU LYS SER LEU LEU LYS ALA ARG LEU PHE ASP SEQRES 3 A 255 GLU ILE ILE TYR TYR GLY ASP SER ALA ARG VAL PRO TYR SEQRES 4 A 255 GLY THR LYS ASP PRO THR THR ILE LYS GLN PHE GLY LEU SEQRES 5 A 255 GLU ALA LEU ASP PHE PHE LYS PRO HIS GLU ILE GLU LEU SEQRES 6 A 255 LEU ILE VAL ALA CYS ASN THR ALA SER ALA LEU ALA LEU SEQRES 7 A 255 GLU GLU MET GLN LYS TYR SER LYS ILE PRO ILE VAL GLY SEQRES 8 A 255 VAL ILE GLU PRO SER ILE LEU ALA ILE LYS ARG GLN VAL SEQRES 9 A 255 GLU ASP LYS ASN ALA PRO ILE LEU VAL LEU GLY THR LYS SEQRES 10 A 255 ALA THR ILE GLN SER ASN ALA TYR ASP ASN ALA LEU LYS SEQRES 11 A 255 GLN GLN GLY TYR LEU ASN ILE SER HIS LEU ALA THR SER SEQRES 12 A 255 LEU PHE VAL PRO LEU ILE GLU GLU SER ILE LEU GLU GLY SEQRES 13 A 255 GLU LEU LEU GLU THR CYS MET HIS TYR TYR PHE THR PRO SEQRES 14 A 255 LEU GLU ILE LEU PRO GLU VAL ILE ILE LEU GLY CYS THR SEQRES 15 A 255 HIS PHE PRO LEU ILE ALA GLN LYS ILE GLU GLY TYR PHE SEQRES 16 A 255 MET GLY HIS PHE ALA LEU PRO THR PRO PRO LEU LEU ILE SEQRES 17 A 255 HIS SER GLY ASP ALA ILE VAL GLU TYR LEU GLN GLN LYS SEQRES 18 A 255 TYR ALA LEU LYS ASN ASN ALA CYS THR PHE PRO LYS VAL SEQRES 19 A 255 GLU PHE HIS ALA SER GLY ASP VAL ILE TRP LEU GLU ARG SEQRES 20 A 255 GLN ALA LYS GLU TRP LEU LYS LEU SEQRES 1 B 255 MET LYS ILE GLY VAL PHE ASP SER GLY VAL GLY GLY PHE SEQRES 2 B 255 SER VAL LEU LYS SER LEU LEU LYS ALA ARG LEU PHE ASP SEQRES 3 B 255 GLU ILE ILE TYR TYR GLY ASP SER ALA ARG VAL PRO TYR SEQRES 4 B 255 GLY THR LYS ASP PRO THR THR ILE LYS GLN PHE GLY LEU SEQRES 5 B 255 GLU ALA LEU ASP PHE PHE LYS PRO HIS GLU ILE GLU LEU SEQRES 6 B 255 LEU ILE VAL ALA CYS ASN THR ALA SER ALA LEU ALA LEU SEQRES 7 B 255 GLU GLU MET GLN LYS TYR SER LYS ILE PRO ILE VAL GLY SEQRES 8 B 255 VAL ILE GLU PRO SER ILE LEU ALA ILE LYS ARG GLN VAL SEQRES 9 B 255 GLU ASP LYS ASN ALA PRO ILE LEU VAL LEU GLY THR LYS SEQRES 10 B 255 ALA THR ILE GLN SER ASN ALA TYR ASP ASN ALA LEU LYS SEQRES 11 B 255 GLN GLN GLY TYR LEU ASN ILE SER HIS LEU ALA THR SER SEQRES 12 B 255 LEU PHE VAL PRO LEU ILE GLU GLU SER ILE LEU GLU GLY SEQRES 13 B 255 GLU LEU LEU GLU THR CYS MET HIS TYR TYR PHE THR PRO SEQRES 14 B 255 LEU GLU ILE LEU PRO GLU VAL ILE ILE LEU GLY CYS THR SEQRES 15 B 255 HIS PHE PRO LEU ILE ALA GLN LYS ILE GLU GLY TYR PHE SEQRES 16 B 255 MET GLY HIS PHE ALA LEU PRO THR PRO PRO LEU LEU ILE SEQRES 17 B 255 HIS SER GLY ASP ALA ILE VAL GLU TYR LEU GLN GLN LYS SEQRES 18 B 255 TYR ALA LEU LYS ASN ASN ALA CYS THR PHE PRO LYS VAL SEQRES 19 B 255 GLU PHE HIS ALA SER GLY ASP VAL ILE TRP LEU GLU ARG SEQRES 20 B 255 GLN ALA LYS GLU TRP LEU LYS LEU HET KRH A1256 33 HET DGL A1257 10 HET DGL B1256 10 HET KRH B1257 33 HETNAM KRH 5-METHYL-3-(1-METHYL-1H-IMIDAZOL-5-YL)-7-(2- HETNAM 2 KRH METHYLPROPYL)-2-(NAPHTHALEN-1-YLMETHYL)-2H-PYRAZOLO[3, HETNAM 3 KRH 4-D]PYRIMIDINE-4,6(5H,7H)-DIONE HETNAM DGL D-GLUTAMIC ACID FORMUL 3 KRH 2(C25 H26 N6 O2) FORMUL 4 DGL 2(C5 H9 N O4) FORMUL 7 HOH *221(H2 O) HELIX 1 1 GLY A 12 ALA A 22 1 11 HELIX 2 2 ASP A 43 LYS A 59 1 17 HELIX 3 3 PRO A 60 GLU A 62 5 3 HELIX 4 4 CYS A 70 ALA A 77 1 8 HELIX 5 5 ALA A 77 SER A 85 1 9 HELIX 6 6 ILE A 93 VAL A 104 1 12 HELIX 7 7 THR A 116 ASN A 123 1 8 HELIX 8 8 ASN A 123 GLN A 132 1 10 HELIX 9 9 LEU A 144 GLU A 151 1 8 HELIX 10 10 GLU A 155 THR A 168 1 14 HELIX 11 11 HIS A 183 LEU A 186 5 4 HELIX 12 12 ILE A 187 PHE A 199 1 13 HELIX 13 13 SER A 210 ALA A 223 1 14 HELIX 14 14 ASP A 241 LYS A 254 1 14 HELIX 15 15 GLY B 9 GLY B 11 5 3 HELIX 16 16 GLY B 12 ALA B 22 1 11 HELIX 17 17 ASP B 43 LYS B 59 1 17 HELIX 18 18 PRO B 60 GLU B 62 5 3 HELIX 19 19 CYS B 70 ALA B 77 1 8 HELIX 20 20 ALA B 77 SER B 85 1 9 HELIX 21 21 ILE B 93 VAL B 104 1 12 HELIX 22 22 THR B 116 SER B 122 1 7 HELIX 23 23 ASN B 123 GLN B 132 1 10 HELIX 24 24 LEU B 144 GLU B 151 1 8 HELIX 25 25 GLU B 155 THR B 168 1 14 HELIX 26 26 HIS B 183 LEU B 186 5 4 HELIX 27 27 ILE B 187 PHE B 199 1 13 HELIX 28 28 HIS B 209 ALA B 223 1 15 HELIX 29 29 ASP B 241 LYS B 254 1 14 SHEET 1 AA 5 ILE A 89 VAL A 90 0 SHEET 2 AA 5 LEU A 66 VAL A 68 1 O LEU A 66 N VAL A 90 SHEET 3 AA 5 LYS A 2 ASP A 7 1 O GLY A 4 N ILE A 67 SHEET 4 AA 5 GLU A 27 GLY A 32 1 O GLU A 27 N ILE A 3 SHEET 5 AA 5 LYS A 233 ALA A 238 1 O LYS A 233 N ILE A 28 SHEET 1 AB 4 ILE A 137 ALA A 141 0 SHEET 2 AB 4 ILE A 111 GLY A 115 1 O ILE A 111 N SER A 138 SHEET 3 AB 4 VAL A 176 GLY A 180 1 O VAL A 176 N LEU A 112 SHEET 4 AB 4 LEU A 206 HIS A 209 1 O LEU A 206 N ILE A 177 SHEET 1 BA 5 ILE B 89 GLY B 91 0 SHEET 2 BA 5 LEU B 66 VAL B 68 1 O LEU B 66 N VAL B 90 SHEET 3 BA 5 LYS B 2 ASP B 7 1 O GLY B 4 N ILE B 67 SHEET 4 BA 5 GLU B 27 GLY B 32 1 O GLU B 27 N ILE B 3 SHEET 5 BA 5 LYS B 233 ALA B 238 1 O LYS B 233 N ILE B 28 SHEET 1 BB 4 ILE B 137 ALA B 141 0 SHEET 2 BB 4 ILE B 111 GLY B 115 1 O ILE B 111 N SER B 138 SHEET 3 BB 4 VAL B 176 LEU B 179 1 O VAL B 176 N LEU B 112 SHEET 4 BB 4 LEU B 206 ILE B 208 1 O LEU B 206 N ILE B 177 CISPEP 1 VAL A 37 PRO A 38 0 -1.40 CISPEP 2 VAL B 37 PRO B 38 0 -2.95 SITE 1 AC1 15 ASP B 7 SER B 8 PRO B 38 TYR B 39 SITE 2 AC1 15 GLY B 40 CYS B 70 ASN B 71 THR B 72 SITE 3 AC1 15 THR B 116 CYS B 181 THR B 182 HIS B 183 SITE 4 AC1 15 HOH B2004 HOH B2039 HOH B2119 SITE 1 AC2 10 VAL A 10 GLY A 11 ILE A 149 GLU A 150 SITE 2 AC2 10 SER A 152 LEU A 186 GLN A 248 TRP A 252 SITE 3 AC2 10 HOH A2068 HOH A2100 SITE 1 AC3 12 VAL B 10 GLY B 11 LYS B 17 ILE B 149 SITE 2 AC3 12 GLU B 150 SER B 152 LEU B 154 LEU B 186 SITE 3 AC3 12 GLN B 248 TRP B 252 HOH B2078 HOH B2120 SITE 1 AC4 15 ASP A 7 SER A 8 PRO A 38 TYR A 39 SITE 2 AC4 15 GLY A 40 CYS A 70 ASN A 71 THR A 72 SITE 3 AC4 15 THR A 116 CYS A 181 THR A 182 HIS A 183 SITE 4 AC4 15 HOH A2005 HOH A2037 HOH A2101 CRYST1 61.933 75.974 108.935 90.00 90.00 90.00 P 21 21 21 8 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 0.016146 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013162 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009180 0.00000