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PDBsum entry 2vcq

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Top Page protein ligands Protein-protein interface(s) links
Isomerase PDB id
2vcq
Jmol
Contents
Protein chain
198 a.a.
Ligands
GSH ×4
D25 ×3
Waters ×363
HEADER    ISOMERASE                               26-SEP-07   2VCQ
TITLE     COMPLEX STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE AT 1.95A.
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: GLUTATHIONE-REQUIRING PROSTAGLANDIN D SYNTHASE;
COMPND   3 CHAIN: A, B, C, D;
COMPND   4 SYNONYM: GLUTATHIONE-DEPENDENT PGD SYNTHETASE,
COMPND   5  PROSTAGLANDIN-H2 D-ISOMERASE, HEMATOPOIETIC PROSTAGLANDIN
COMPND   6  D SYNTHASE, H-PGDS, PROSTAGLANDIN D2 SYNTHASE;
COMPND   7 EC: 5.3.99.2;
COMPND   8 ENGINEERED: YES;
COMPND   9 OTHER_DETAILS: THE PROTEIN CONTAIN A GLUTATHIONE CO-FACTOR.
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)
KEYWDS    PROSTAGLANDIN BIOSYNTHESIS, FATTY ACID BIOSYNTHESIS,
KEYWDS   2 PROSTAGLANDIN D2 SYNTHASE, PGDS, ASTHMA, CYTOPLASM,
KEYWDS   3 ISOMERASE, LIPID SYNTHESIS
EXPDTA    X-RAY DIFFRACTION
AUTHOR    M.HOHWY,L.SPADOLA,B.LUNDQUIST,K.VON WACHENFELDT,
AUTHOR   2 S.PERSDOTTER,P.HAWTIN,J.DAHMEN,I.GROTH-CLAUSEN,
AUTHOR   3 R.H.A.FOLMER,K.EDMAN
REVDAT   2   24-FEB-09 2VCQ    1       VERSN
REVDAT   1   15-APR-08 2VCQ    0
JRNL        AUTH   M.HOHWY,L.SPADOLA,B.LUNDQUIST,P.HAWTIN,J.DAHMEN,
JRNL        AUTH 2 I.GROTH-CLAUSEN,E.NILSSON,S.PERSDOTTER,
JRNL        AUTH 3 K.VON WACHENFELDT,R.H.A.FOLMER,K.EDMAN
JRNL        TITL   NOVEL PROSTAGLANDIN D SYNTHASE INHIBITORS
JRNL        TITL 2 GENERATED BY FRAGMENT-BASED DRUG DESIGN.
JRNL        REF    J.MED.CHEM.                   V.  51  2178 2008
JRNL        REFN                   ISSN 0022-2623
JRNL        PMID   18341273
JRNL        DOI    10.1021/JM701509K
REMARK   2
REMARK   2 RESOLUTION.    1.95 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5.2.0019
REMARK   3   AUTHORS     : MURSHUDOV,VAGIN,DODSON
REMARK   3
REMARK   3    REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 50.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL
REMARK   3   COMPLETENESS FOR RANGE        (%) : 96.1
REMARK   3   NUMBER OF REFLECTIONS             : 51074
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) : 0.197
REMARK   3   R VALUE            (WORKING SET) : 0.195
REMARK   3   FREE R VALUE                     : 0.237
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.100
REMARK   3   FREE R VALUE TEST SET COUNT      : 2752
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) : 1.95
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.00
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 3694
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 93.78
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2420
REMARK   3   BIN FREE R VALUE SET COUNT          : 184
REMARK   3   BIN FREE R VALUE                    : 0.2640
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 6476
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 128
REMARK   3   SOLVENT ATOMS            : 363
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 24.57
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : 0.86000
REMARK   3    B22 (A**2) : 0.86000
REMARK   3    B33 (A**2) : -1.72000
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): 0.215
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.176
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.126
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.350
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.945
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.922
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  6773 ; 0.010 ; 0.022
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  9201 ; 1.330 ; 1.970
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   778 ; 2.868 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   329 ;29.422 ;24.225
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):  1154 ;11.606 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    40 ;13.319 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):  1003 ; 0.097 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  5163 ; 0.005 ; 0.020
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  3222 ; 0.196 ; 0.200
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  4613 ; 0.309 ; 0.200
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):   463 ; 0.136 ; 0.200
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):    96 ; 0.191 ; 0.200
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):    25 ; 0.151 ; 0.200
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):  4061 ; 0.725 ; 1.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  6383 ; 1.180 ; 2.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  3161 ; 1.585 ; 3.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  2818 ; 2.388 ; 4.500
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  : NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELLING.
REMARK   3   METHOD USED : BABINET MODEL WITH MASK
REMARK   3   PARAMETERS FOR MASK CALCULATION
REMARK   3   VDW PROBE RADIUS   : 1.40
REMARK   3   ION PROBE RADIUS   : 0.80
REMARK   3   SHRINKAGE RADIUS   : 0.80
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 2VCQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-SEP-07.
REMARK 100 THE PDBE ID CODE IS EBI-33974.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 22-SEP-04
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 8.4
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : ESRF
REMARK 200  BEAMLINE                       : ID29
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.975
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : MIRRORS
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200  DATA SCALING SOFTWARE          : SCALA
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 4135
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.95
REMARK 200  RESOLUTION RANGE LOW       (A) : 86.00
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 2.9
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 98.5
REMARK 200  DATA REDUNDANCY                : 2.5
REMARK 200  R MERGE                    (I) : 0.08
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 7.30
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.00
REMARK 200  COMPLETENESS FOR SHELL     (%) : 99.9
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.4
REMARK 200  R MERGE FOR SHELL          (I) : 0.33
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : 2.90
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 1PD2
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 44
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.2
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG6000, 1% DIOXANE, 5MM
REMARK 280  DTT, 5MM GSH, 0.05 M TRISHCL PH8.4
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X+1/2,-Y+1/2,Z+1/2
REMARK 290       3555   -Y,X+1/2,Z+1/4
REMARK 290       4555   Y+1/2,-X,Z+3/4
REMARK 290       5555   X+1/2,Y+1/2,Z+1/2
REMARK 290       6555   -X,-Y,Z
REMARK 290       7555   -Y+1/2,X,Z+3/4
REMARK 290       8555   Y,-X+1/2,Z+1/4
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       60.86000
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000       60.86000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       52.78300
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       60.86000
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       26.39150
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       60.86000
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       79.17450
REMARK 290   SMTRY1   5  1.000000  0.000000  0.000000       60.86000
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       60.86000
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000       52.78300
REMARK 290   SMTRY1   6 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   7  0.000000 -1.000000  0.000000       60.86000
REMARK 290   SMTRY2   7  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   7  0.000000  0.000000  1.000000       79.17450
REMARK 290   SMTRY1   8  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY2   8 -1.000000  0.000000  0.000000       60.86000
REMARK 290   SMTRY3   8  0.000000  0.000000  1.000000       26.39150
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 350
REMARK 350 GENERATING THE BIOMOLECULE
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: PQS
REMARK 350 TOTAL BURIED SURFACE AREA: 3070 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 22180 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.1 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 350
REMARK 350 BIOMOLECULE:  2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PQS
REMARK 350 TOTAL BURIED SURFACE AREA: 3310 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 21680 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.9 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 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     MET A     1
REMARK 465     MET B     1
REMARK 465     MET C     1
REMARK 465     MET D     1
REMARK 465     SER D   100
REMARK 465     CYS D   101
REMARK 465     PHE D   102
REMARK 465     PRO D   103
REMARK 465     TRP D   104
REMARK 465     ALA D   105
REMARK 465     GLU D   106
REMARK 465     LYS D   107
REMARK 465     LYS D   108
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 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    GLN A  63      104.85     74.59
REMARK 500    TYR A 122      -69.51   -103.75
REMARK 500    GLN B  63      105.80     74.00
REMARK 500    GLN C  63       97.06     75.57
REMARK 500    GLN D  63      101.21     74.54
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GSH A1200
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GSH B1200
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GSH C1200
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GSH D1200
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D25 A1201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D25 B1201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D25 C1201
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1V40   RELATED DB: PDB
REMARK 900  FIRST INHIBITOR COMPLEX STRUCTURE OF HUMAN
REMARK 900  HEMATOPOIETICPROSTAGLANDIN D SYNTHASE
REMARK 900 RELATED ID: 1IYH   RELATED DB: PDB
REMARK 900  CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN
REMARK 900   D SYNTHASE
REMARK 900 RELATED ID: 1IYI   RELATED DB: PDB
REMARK 900  CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN
REMARK 900   D SYNTHASE
DBREF  2VCQ A    1   199  UNP    O60760   PTGD2_HUMAN      1    199
DBREF  2VCQ B    1   199  UNP    O60760   PTGD2_HUMAN      1    199
DBREF  2VCQ C    1   199  UNP    O60760   PTGD2_HUMAN      1    199
DBREF  2VCQ D    1   199  UNP    O60760   PTGD2_HUMAN      1    199
SEQRES   1 A  199  MET PRO ASN TYR LYS LEU THR TYR PHE ASN MET ARG GLY
SEQRES   2 A  199  ARG ALA GLU ILE ILE ARG TYR ILE PHE ALA TYR LEU ASP
SEQRES   3 A  199  ILE GLN TYR GLU ASP HIS ARG ILE GLU GLN ALA ASP TRP
SEQRES   4 A  199  PRO GLU ILE LYS SER THR LEU PRO PHE GLY LYS ILE PRO
SEQRES   5 A  199  ILE LEU GLU VAL ASP GLY LEU THR LEU HIS GLN SER LEU
SEQRES   6 A  199  ALA ILE ALA ARG TYR LEU THR LYS ASN THR ASP LEU ALA
SEQRES   7 A  199  GLY ASN THR GLU MET GLU GLN CYS HIS VAL ASP ALA ILE
SEQRES   8 A  199  VAL ASP THR LEU ASP ASP PHE MET SER CYS PHE PRO TRP
SEQRES   9 A  199  ALA GLU LYS LYS GLN ASP VAL LYS GLU GLN MET PHE ASN
SEQRES  10 A  199  GLU LEU LEU THR TYR ASN ALA PRO HIS LEU MET GLN ASP
SEQRES  11 A  199  LEU ASP THR TYR LEU GLY GLY ARG GLU TRP LEU ILE GLY
SEQRES  12 A  199  ASN SER VAL THR TRP ALA ASP PHE TYR TRP GLU ILE CYS
SEQRES  13 A  199  SER THR THR LEU LEU VAL PHE LYS PRO ASP LEU LEU ASP
SEQRES  14 A  199  ASN HIS PRO ARG LEU VAL THR LEU ARG LYS LYS VAL GLN
SEQRES  15 A  199  ALA ILE PRO ALA VAL ALA ASN TRP ILE LYS ARG ARG PRO
SEQRES  16 A  199  GLN THR LYS LEU
SEQRES   1 B  199  MET PRO ASN TYR LYS LEU THR TYR PHE ASN MET ARG GLY
SEQRES   2 B  199  ARG ALA GLU ILE ILE ARG TYR ILE PHE ALA TYR LEU ASP
SEQRES   3 B  199  ILE GLN TYR GLU ASP HIS ARG ILE GLU GLN ALA ASP TRP
SEQRES   4 B  199  PRO GLU ILE LYS SER THR LEU PRO PHE GLY LYS ILE PRO
SEQRES   5 B  199  ILE LEU GLU VAL ASP GLY LEU THR LEU HIS GLN SER LEU
SEQRES   6 B  199  ALA ILE ALA ARG TYR LEU THR LYS ASN THR ASP LEU ALA
SEQRES   7 B  199  GLY ASN THR GLU MET GLU GLN CYS HIS VAL ASP ALA ILE
SEQRES   8 B  199  VAL ASP THR LEU ASP ASP PHE MET SER CYS PHE PRO TRP
SEQRES   9 B  199  ALA GLU LYS LYS GLN ASP VAL LYS GLU GLN MET PHE ASN
SEQRES  10 B  199  GLU LEU LEU THR TYR ASN ALA PRO HIS LEU MET GLN ASP
SEQRES  11 B  199  LEU ASP THR TYR LEU GLY GLY ARG GLU TRP LEU ILE GLY
SEQRES  12 B  199  ASN SER VAL THR TRP ALA ASP PHE TYR TRP GLU ILE CYS
SEQRES  13 B  199  SER THR THR LEU LEU VAL PHE LYS PRO ASP LEU LEU ASP
SEQRES  14 B  199  ASN HIS PRO ARG LEU VAL THR LEU ARG LYS LYS VAL GLN
SEQRES  15 B  199  ALA ILE PRO ALA VAL ALA ASN TRP ILE LYS ARG ARG PRO
SEQRES  16 B  199  GLN THR LYS LEU
SEQRES   1 C  199  MET PRO ASN TYR LYS LEU THR TYR PHE ASN MET ARG GLY
SEQRES   2 C  199  ARG ALA GLU ILE ILE ARG TYR ILE PHE ALA TYR LEU ASP
SEQRES   3 C  199  ILE GLN TYR GLU ASP HIS ARG ILE GLU GLN ALA ASP TRP
SEQRES   4 C  199  PRO GLU ILE LYS SER THR LEU PRO PHE GLY LYS ILE PRO
SEQRES   5 C  199  ILE LEU GLU VAL ASP GLY LEU THR LEU HIS GLN SER LEU
SEQRES   6 C  199  ALA ILE ALA ARG TYR LEU THR LYS ASN THR ASP LEU ALA
SEQRES   7 C  199  GLY ASN THR GLU MET GLU GLN CYS HIS VAL ASP ALA ILE
SEQRES   8 C  199  VAL ASP THR LEU ASP ASP PHE MET SER CYS PHE PRO TRP
SEQRES   9 C  199  ALA GLU LYS LYS GLN ASP VAL LYS GLU GLN MET PHE ASN
SEQRES  10 C  199  GLU LEU LEU THR TYR ASN ALA PRO HIS LEU MET GLN ASP
SEQRES  11 C  199  LEU ASP THR TYR LEU GLY GLY ARG GLU TRP LEU ILE GLY
SEQRES  12 C  199  ASN SER VAL THR TRP ALA ASP PHE TYR TRP GLU ILE CYS
SEQRES  13 C  199  SER THR THR LEU LEU VAL PHE LYS PRO ASP LEU LEU ASP
SEQRES  14 C  199  ASN HIS PRO ARG LEU VAL THR LEU ARG LYS LYS VAL GLN
SEQRES  15 C  199  ALA ILE PRO ALA VAL ALA ASN TRP ILE LYS ARG ARG PRO
SEQRES  16 C  199  GLN THR LYS LEU
SEQRES   1 D  199  MET PRO ASN TYR LYS LEU THR TYR PHE ASN MET ARG GLY
SEQRES   2 D  199  ARG ALA GLU ILE ILE ARG TYR ILE PHE ALA TYR LEU ASP
SEQRES   3 D  199  ILE GLN TYR GLU ASP HIS ARG ILE GLU GLN ALA ASP TRP
SEQRES   4 D  199  PRO GLU ILE LYS SER THR LEU PRO PHE GLY LYS ILE PRO
SEQRES   5 D  199  ILE LEU GLU VAL ASP GLY LEU THR LEU HIS GLN SER LEU
SEQRES   6 D  199  ALA ILE ALA ARG TYR LEU THR LYS ASN THR ASP LEU ALA
SEQRES   7 D  199  GLY ASN THR GLU MET GLU GLN CYS HIS VAL ASP ALA ILE
SEQRES   8 D  199  VAL ASP THR LEU ASP ASP PHE MET SER CYS PHE PRO TRP
SEQRES   9 D  199  ALA GLU LYS LYS GLN ASP VAL LYS GLU GLN MET PHE ASN
SEQRES  10 D  199  GLU LEU LEU THR TYR ASN ALA PRO HIS LEU MET GLN ASP
SEQRES  11 D  199  LEU ASP THR TYR LEU GLY GLY ARG GLU TRP LEU ILE GLY
SEQRES  12 D  199  ASN SER VAL THR TRP ALA ASP PHE TYR TRP GLU ILE CYS
SEQRES  13 D  199  SER THR THR LEU LEU VAL PHE LYS PRO ASP LEU LEU ASP
SEQRES  14 D  199  ASN HIS PRO ARG LEU VAL THR LEU ARG LYS LYS VAL GLN
SEQRES  15 D  199  ALA ILE PRO ALA VAL ALA ASN TRP ILE LYS ARG ARG PRO
SEQRES  16 D  199  GLN THR LYS LEU
HET    GSH  A1200      20
HET    GSH  B1200      20
HET    GSH  C1200      20
HET    GSH  D1200      20
HET    D25  A1201      16
HET    D25  B1201      16
HET    D25  C1201      16
HETNAM     D25 3-PHENYL-5-(1H-PYRAZOL-3-YL)ISOXAZOLE
HETNAM     GSH GLUTATHIONE
FORMUL   5  D25    3(C12 H9 N3 O1)
FORMUL   6  GSH    4(C10 H17 N3 O6 S)
FORMUL   7  HOH   *363(H2 O1)
HELIX    1   1 ARG A   12  ARG A   14  5                                   3
HELIX    2   2 ALA A   15  ASP A   26  1                                  12
HELIX    3   3 GLU A   35  ALA A   37  5                                   3
HELIX    4   4 ASP A   38  LEU A   46  1                                   9
HELIX    5   5 GLN A   63  LYS A   73  1                                  11
HELIX    6   6 THR A   75  GLY A   79  5                                   5
HELIX    7   7 THR A   81  SER A  100  1                                  20
HELIX    8   8 LYS A  108  TYR A  122  1                                  15
HELIX    9   9 TYR A  122  GLY A  136  1                                  15
HELIX   10  10 THR A  147  LYS A  164  1                                  18
HELIX   11  11 HIS A  171  ALA A  183  1                                  13
HELIX   12  12 ILE A  184  ARG A  194  1                                  11
HELIX   13  13 ALA B   15  LEU B   25  1                                  11
HELIX   14  14 GLU B   35  ALA B   37  5                                   3
HELIX   15  15 ASP B   38  SER B   44  1                                   7
HELIX   16  16 GLN B   63  LYS B   73  1                                  11
HELIX   17  17 THR B   81  SER B  100  1                                  20
HELIX   18  18 LYS B  108  ASN B  123  1                                  16
HELIX   19  19 ASN B  123  GLY B  136  1                                  14
HELIX   20  20 THR B  147  LYS B  164  1                                  18
HELIX   21  21 HIS B  171  ALA B  183  1                                  13
HELIX   22  22 ILE B  184  ARG B  194  1                                  11
HELIX   23  23 ALA C   15  ASP C   26  1                                  12
HELIX   24  24 ASP C   38  SER C   44  1                                   7
HELIX   25  25 GLN C   63  LYS C   73  1                                  11
HELIX   26  26 THR C   81  PHE C  102  1                                  22
HELIX   27  27 LYS C  108  ASN C  123  1                                  16
HELIX   28  28 ASN C  123  GLY C  136  1                                  14
HELIX   29  29 THR C  147  LYS C  164  1                                  18
HELIX   30  30 HIS C  171  ILE C  184  1                                  14
HELIX   31  31 ILE C  184  ARG C  194  1                                  11
HELIX   32  32 ALA D   15  ASP D   26  1                                  12
HELIX   33  33 GLU D   35  ALA D   37  5                                   3
HELIX   34  34 ASP D   38  SER D   44  1                                   7
HELIX   35  35 GLN D   63  LYS D   73  1                                  11
HELIX   36  36 THR D   81  ASP D   97  1                                  17
HELIX   37  37 GLN D  109  ASN D  123  1                                  15
HELIX   38  38 ASN D  123  LEU D  135  1                                  13
HELIX   39  39 THR D  147  LYS D  164  1                                  18
HELIX   40  40 HIS D  171  ALA D  183  1                                  13
HELIX   41  41 ILE D  184  ARG D  194  1                                  11
SHEET    1  AA 4 GLU A  30  ILE A  34  0
SHEET    2  AA 4 TYR A   4  PHE A   9  1  O  TYR A   4   N  GLU A  30
SHEET    3  AA 4 ILE A  53  VAL A  56 -1  O  ILE A  53   N  THR A   7
SHEET    4  AA 4 LEU A  59  HIS A  62 -1  O  LEU A  59   N  VAL A  56
SHEET    1  BA 4 GLU B  30  ILE B  34  0
SHEET    2  BA 4 TYR B   4  PHE B   9  1  O  TYR B   4   N  GLU B  30
SHEET    3  BA 4 ILE B  53  VAL B  56 -1  O  ILE B  53   N  THR B   7
SHEET    4  BA 4 LEU B  59  HIS B  62 -1  O  LEU B  59   N  VAL B  56
SHEET    1  CA 4 GLU C  30  ILE C  34  0
SHEET    2  CA 4 LYS C   5  PHE C   9  1  O  LEU C   6   N  HIS C  32
SHEET    3  CA 4 ILE C  53  VAL C  56 -1  O  ILE C  53   N  THR C   7
SHEET    4  CA 4 LEU C  59  HIS C  62 -1  O  LEU C  59   N  VAL C  56
SHEET    1  DA 4 GLU D  30  ILE D  34  0
SHEET    2  DA 4 TYR D   4  PHE D   9  1  O  TYR D   4   N  GLU D  30
SHEET    3  DA 4 ILE D  53  VAL D  56 -1  O  ILE D  53   N  THR D   7
SHEET    4  DA 4 LEU D  59  HIS D  62 -1  O  LEU D  59   N  VAL D  56
CISPEP   1 ILE A   51    PRO A   52          0         3.40
CISPEP   2 ILE B   51    PRO B   52          0         6.21
CISPEP   3 ILE C   51    PRO C   52          0         4.35
CISPEP   4 ILE D   51    PRO D   52          0         5.14
SITE     1 AC1 11 TYR A   8  ARG A  14  TRP A  39  LYS A  43
SITE     2 AC1 11 LYS A  50  ILE A  51  GLN A  63  SER A  64
SITE     3 AC1 11 HOH A2005  HOH A2032  ASP B  97
SITE     1 AC2 15 ASP A  97  TYR B   8  ARG B  14  TRP B  39
SITE     2 AC2 15 LYS B  43  LYS B  50  ILE B  51  GLN B  63
SITE     3 AC2 15 SER B  64  D25 B1201  HOH B2059  HOH B2060
SITE     4 AC2 15 HOH B2103  HOH B2104  HOH B2105
SITE     1 AC3 13 TYR C   8  ARG C  14  TRP C  39  LYS C  43
SITE     2 AC3 13 LYS C  50  ILE C  51  PRO C  52  GLN C  63
SITE     3 AC3 13 SER C  64  D25 C1201  HOH C2023  HOH C2080
SITE     4 AC3 13 ASP D  97
SITE     1 AC4 13 ASP C  97  TYR D   8  ARG D  14  TRP D  39
SITE     2 AC4 13 LYS D  43  LYS D  50  ILE D  51  PRO D  52
SITE     3 AC4 13 GLN D  63  SER D  64  HOH D2081  HOH D2082
SITE     4 AC4 13 HOH D2083
SITE     1 AC5  4 ARG A  14  MET A  99  TYR A 152  HOH A2095
SITE     1 AC6  8 MET B  11  GLY B  13  ARG B  14  MET B  99
SITE     2 AC6  8 TRP B 104  TYR B 152  GSH B1200  HOH B2101
SITE     1 AC7  9 MET C  11  GLY C  13  ARG C  14  MET C  99
SITE     2 AC7  9 TRP C 104  TYR C 152  LEU C 199  GSH C1200
SITE     3 AC7  9 HOH C2058
CRYST1  121.720  121.720  105.566  90.00  90.00  90.00 I 41         32
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      0.008216  0.000000  0.000000        0.00000
SCALE2      0.000000  0.008216  0.000000        0.00000
SCALE3      0.000000  0.000000  0.009473        0.00000
      
PROCHECK
Go to PROCHECK summary
 References