HEADER ISOMERASE 27-SEP-07 2VCX
TITLE COMPLEX STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE AT 2.1A.
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, PROSTAGLANDIN-H2 D-
COMPND 5 ISOMERASE, HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE, H-PGDS,
COMPND 6 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, PROSTAGLANDIN D2
KEYWDS 2 SYNTHASE, PGDS, ASTHMA, CYTOPLASM, ISOMERASE, LIPID SYNTHESIS
EXPDTA X-RAY DIFFRACTION
AUTHOR M.HOHWY,L.SPADOLA,B.LUNDQUIST,K.VON WACHENFELDT,S.PERSDOTTER,
AUTHOR 2 P.HAWTIN,J.DAHMEN,I.GROTH-CLAUSEN,R.H.A.FOLMER,K.EDMAN
REVDAT 3 13-DEC-23 2VCX 1 LINK
REVDAT 2 24-FEB-09 2VCX 1 VERSN
REVDAT 1 15-APR-08 2VCX 0
JRNL AUTH M.HOHWY,L.SPADOLA,B.LUNDQUIST,P.HAWTIN,J.DAHMEN,
JRNL AUTH 2 I.GROTH-CLAUSEN,E.NILSSON,S.PERSDOTTER,K.VON WACHENFELDT,
JRNL AUTH 3 R.H.A.FOLMER,K.EDMAN
JRNL TITL NOVEL PROSTAGLANDIN D SYNTHASE INHIBITORS GENERATED BY
JRNL TITL 2 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. 2.10 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
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) : 2.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9
REMARK 3 NUMBER OF REFLECTIONS : 42575
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) : 0.199
REMARK 3 R VALUE (WORKING SET) : 0.196
REMARK 3 FREE R VALUE : 0.248
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 2271
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) : 2.10
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2953
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.81
REMARK 3 BIN R VALUE (WORKING SET) : 0.2290
REMARK 3 BIN FREE R VALUE SET COUNT : 170
REMARK 3 BIN FREE R VALUE : 0.3080
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6474
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 130
REMARK 3 SOLVENT ATOMS : 270
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.40
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.31000
REMARK 3 B22 (A**2) : 0.31000
REMARK 3 B33 (A**2) : -0.61000
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): 0.287
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.216
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.148
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.439
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6775 ; 0.011 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9207 ; 1.370 ; 1.969
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 778 ; 2.838 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 327 ;30.317 ;24.128
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1146 ;12.046 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;13.665 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1002 ; 0.099 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5168 ; 0.005 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3194 ; 0.199 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4608 ; 0.310 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 423 ; 0.149 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.006 ; 0.200
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 67 ; 0.177 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.117 ; 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): 4071 ; 0.709 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6384 ; 1.181 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3178 ; 1.660 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2823 ; 2.512 ; 4.500
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 : 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 2VCX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-SEP-07.
REMARK 100 THE DEPOSITION ID IS D_1290033995.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-DEC-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 : ID14-4
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46651
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100
REMARK 200 RESOLUTION RANGE LOW (A) : 88.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.800
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 3.200
REMARK 200 R MERGE (I) : 0.10000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 3.20
REMARK 200 R MERGE FOR SHELL (I) : 0.10000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800
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 (%): 45.96
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000 30%, TCEP 5MM, GSH 5MM,
REMARK 280 DIOXANE 1%, MGCL2 5MM, TRISHCL (PH8.4) 50 MM
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 61.90650
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 61.90650
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.14850
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 61.90650
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.57425
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 61.90650
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 79.72275
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 61.90650
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.90650
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 53.14850
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 61.90650
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 79.72275
REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 61.90650
REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 26.57425
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 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: 2980 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 22510 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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: 2330 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 21070 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.1 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 GLU C 106
REMARK 465 LYS C 107
REMARK 465 LYS C 108
REMARK 465 GLN C 109
REMARK 465 ASP C 110
REMARK 465 VAL C 111
REMARK 465 LYS C 112
REMARK 465 GLU C 113
REMARK 465 GLN C 114
REMARK 465 MET D 1
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 GLN A 63 109.63 70.86
REMARK 500 TYR A 122 -61.66 -108.63
REMARK 500 GLN B 63 108.06 71.56
REMARK 500 GLN C 63 104.44 73.48
REMARK 500 ASP D 57 49.66 38.57
REMARK 500 GLN D 63 104.80 74.32
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 MG A1200 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A2032 O
REMARK 620 2 HOH A2036 O 98.4
REMARK 620 3 HOH A2037 O 101.6 80.6
REMARK 620 4 HOH B2043 O 168.5 84.2 89.8
REMARK 620 5 HOH B2044 O 98.2 162.5 90.6 80.6
REMARK 620 6 HOH B2046 O 79.6 95.9 176.3 89.0 92.6
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG C1200 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH C2021 O
REMARK 620 2 HOH C2026 O 91.0
REMARK 620 3 HOH C2027 O 90.8 90.1
REMARK 620 4 HOH D2022 O 91.4 175.7 86.3
REMARK 620 5 HOH D2025 O 171.5 85.8 97.1 92.3
REMARK 620 6 HOH D2028 O 82.0 92.2 172.5 91.7 90.2
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1200
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GSH A1201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GSH B1200
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D26 B1201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C1200
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GSH C1201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D26 C1202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GSH D1200
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D26 D1201
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: 2VCQ RELATED DB: PDB
REMARK 900 COMPLEX STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE AT 1.95A.
REMARK 900 RELATED ID: 2VCW RELATED DB: PDB
REMARK 900 COMPLEX STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE AT 1.95A.
REMARK 900 RELATED ID: 1IYH RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE
REMARK 900 RELATED ID: 1IYI RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE
REMARK 900 RELATED ID: 2VCZ RELATED DB: PDB
REMARK 900 COMPLEX STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE AT 1.95A.
REMARK 900 RELATED ID: 2VD0 RELATED DB: PDB
REMARK 900 COMPLEX STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE AT 2.2A.
DBREF 2VCX A 1 199 UNP O60760 PTGD2_HUMAN 1 199
DBREF 2VCX B 1 199 UNP O60760 PTGD2_HUMAN 1 199
DBREF 2VCX C 1 199 UNP O60760 PTGD2_HUMAN 1 199
DBREF 2VCX 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 MG A1200 1
HET GSH A1201 20
HET GSH B1200 20
HET D26 B1201 16
HET MG C1200 1
HET GSH C1201 20
HET D26 C1202 16
HET GSH D1200 20
HET D26 D1201 16
HETNAM MG MAGNESIUM ION
HETNAM GSH GLUTATHIONE
HETNAM D26 PHENYL-5-(1H-PYRAZOL-3-YL)-1,3-THIAZOLE
FORMUL 5 MG 2(MG 2+)
FORMUL 6 GSH 4(C10 H17 N3 O6 S)
FORMUL 8 D26 3(C12 H9 N3 S)
FORMUL 14 HOH *270(H2 O)
HELIX 1 1 ALA A 15 LEU A 25 1 11
HELIX 2 2 GLU A 35 ALA A 37 5 3
HELIX 3 3 ASP A 38 THR A 45 1 8
HELIX 4 4 GLN A 63 LYS A 73 1 11
HELIX 5 5 THR A 75 GLY A 79 5 5
HELIX 6 6 THR A 81 SER A 100 1 20
HELIX 7 7 LYS A 108 TYR A 122 1 15
HELIX 8 8 TYR A 122 GLY A 136 1 15
HELIX 9 9 THR A 147 LYS A 164 1 18
HELIX 10 10 HIS A 171 ALA A 183 1 13
HELIX 11 11 ILE A 184 ARG A 194 1 11
HELIX 12 12 ARG B 12 ARG B 14 5 3
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 ILE B 184 1 14
HELIX 22 22 ILE B 184 ARG B 194 1 11
HELIX 23 23 ARG C 12 ARG C 14 5 3
HELIX 24 24 ALA C 15 LEU C 25 1 11
HELIX 25 25 ASP C 38 LEU C 46 1 9
HELIX 26 26 GLN C 63 LYS C 73 1 11
HELIX 27 27 THR C 81 CYS C 101 1 21
HELIX 28 28 MET C 115 GLY C 136 1 22
HELIX 29 29 THR C 147 LYS C 164 1 18
HELIX 30 30 HIS C 171 ALA C 183 1 13
HELIX 31 31 ILE C 184 ARG C 194 1 11
HELIX 32 32 ALA D 15 LEU D 25 1 11
HELIX 33 33 ASP D 38 SER D 44 1 7
HELIX 34 34 GLN D 63 LYS D 73 1 11
HELIX 35 35 THR D 81 SER D 100 1 20
HELIX 36 36 LYS D 108 ASN D 123 1 16
HELIX 37 37 ASN D 123 GLY D 136 1 14
HELIX 38 38 THR D 147 LYS D 164 1 18
HELIX 39 39 HIS D 171 ILE D 184 1 14
HELIX 40 40 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 TYR C 4 PHE C 9 1 O TYR C 4 N GLU C 30
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 LYS D 5 PHE D 9 1 O LEU D 6 N HIS D 32
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
LINK MG MG A1200 O HOH A2032 1555 1555 2.23
LINK MG MG A1200 O HOH A2036 1555 1555 2.04
LINK MG MG A1200 O HOH A2037 1555 1555 1.98
LINK MG MG A1200 O HOH B2043 1555 1555 2.03
LINK MG MG A1200 O HOH B2044 1555 1555 2.08
LINK MG MG A1200 O HOH B2046 1555 1555 2.11
LINK MG MG C1200 O HOH C2021 1555 1555 1.99
LINK MG MG C1200 O HOH C2026 1555 1555 2.06
LINK MG MG C1200 O HOH C2027 1555 1555 2.09
LINK MG MG C1200 O HOH D2022 1555 1555 2.03
LINK MG MG C1200 O HOH D2025 1555 1555 2.01
LINK MG MG C1200 O HOH D2028 1555 1555 2.17
CISPEP 1 ILE A 51 PRO A 52 0 6.16
CISPEP 2 ILE B 51 PRO B 52 0 7.17
CISPEP 3 ILE C 51 PRO C 52 0 4.15
CISPEP 4 ILE D 51 PRO D 52 0 5.48
SITE 1 AC1 6 HOH A2032 HOH A2036 HOH A2037 HOH B2043
SITE 2 AC1 6 HOH B2044 HOH B2046
SITE 1 AC2 12 TYR A 8 ARG A 14 TRP A 39 LYS A 43
SITE 2 AC2 12 LYS A 50 ILE A 51 GLN A 63 SER A 64
SITE 3 AC2 12 HOH A2004 HOH A2015 HOH A2035 ASP B 97
SITE 1 AC3 12 ASP A 97 TYR B 8 ARG B 14 TRP B 39
SITE 2 AC3 12 LYS B 43 LYS B 50 ILE B 51 GLN B 63
SITE 3 AC3 12 SER B 64 D26 B1201 HOH B2087 HOH B2088
SITE 1 AC4 8 MET B 11 GLY B 13 ARG B 14 MET B 99
SITE 2 AC4 8 TRP B 104 TYR B 152 GSH B1200 HOH B2085
SITE 1 AC5 6 HOH C2021 HOH C2026 HOH C2027 HOH D2022
SITE 2 AC5 6 HOH D2025 HOH D2028
SITE 1 AC6 14 TYR C 8 ARG C 14 TRP C 39 LYS C 43
SITE 2 AC6 14 LYS C 50 ILE C 51 GLN C 63 SER C 64
SITE 3 AC6 14 D26 C1202 HOH C2014 HOH C2025 HOH C2029
SITE 4 AC6 14 HOH C2061 ASP D 97
SITE 1 AC7 9 MET C 11 GLY C 13 ARG C 14 ASP C 96
SITE 2 AC7 9 MET C 99 TRP C 104 TYR C 152 GSH C1201
SITE 3 AC7 9 HOH C2060
SITE 1 AC8 14 ASP C 97 TYR D 8 ARG D 14 TRP D 39
SITE 2 AC8 14 LYS D 43 LYS D 50 ILE D 51 PRO D 52
SITE 3 AC8 14 GLN D 63 SER D 64 D26 D1201 HOH D2005
SITE 4 AC8 14 HOH D2013 HOH D2026
SITE 1 AC9 7 GLY D 13 ARG D 14 MET D 99 TRP D 104
SITE 2 AC9 7 TYR D 152 GSH D1200 HOH D2044
CRYST1 123.813 123.813 106.297 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 0.008077 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008077 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009408 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
