PDB Short entry for 2VD1 HEADER ISOMERASE 28-SEP-07 2VD1 TITLE COMPLEX STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE AT 2.25A. 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 2VD1 1 LINK REVDAT 2 24-FEB-09 2VD1 1 VERSN REVDAT 1 15-APR-08 2VD1 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. 2.25 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 34207 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) : 0.184 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1811 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2355 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE SET COUNT : 122 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6418 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 105 REMARK 3 SOLVENT ATOMS : 349 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.48000 REMARK 3 B22 (A**2) : 0.48000 REMARK 3 B33 (A**2) : -0.96000 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): 0.434 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.266 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.183 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.174 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.881 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6686 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9088 ; 1.467 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 772 ; 2.995 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 324 ;30.454 ;24.167 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1140 ;12.536 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;13.949 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 996 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5085 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3220 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4573 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 467 ; 0.170 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.098 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 78 ; 0.194 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.132 ; 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): 4030 ; 0.745 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6334 ; 1.246 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3116 ; 1.600 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2754 ; 2.422 ; 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 2VD1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1290034001. 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 : 37285 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 87.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 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 (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 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 61.76050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 61.76050 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.14450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 61.76050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.57225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 61.76050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 79.71675 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 61.76050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.76050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 53.14450 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 61.76050 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 79.71675 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 61.76050 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 26.57225 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: 3180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.6 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: 2100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.2 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 PHE C 102 REMARK 465 PRO C 103 REMARK 465 TRP C 104 REMARK 465 ALA C 105 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 C 115 REMARK 465 PHE C 116 REMARK 465 MET D 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ALA C 78 O HOH C 2039 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 LEU A 95 CA - CB - CG ANGL. DEV. = 14.2 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 GLN A 63 108.66 71.27 REMARK 500 TYR A 122 -71.50 -107.64 REMARK 500 ASP B 57 20.76 48.63 REMARK 500 GLN B 63 108.27 72.33 REMARK 500 ALA B 105 52.93 -111.45 REMARK 500 PRO C 47 -37.12 -39.57 REMARK 500 GLN C 63 104.23 76.32 REMARK 500 MET C 99 5.82 -67.17 REMARK 500 TYR C 122 -69.18 -97.94 REMARK 500 LYS C 164 79.38 -150.14 REMARK 500 ASP D 57 40.30 37.83 REMARK 500 GLN D 63 104.64 77.83 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 B1201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2043 O REMARK 620 2 HOH A2046 O 89.5 REMARK 620 3 HOH A2048 O 89.8 75.4 REMARK 620 4 HOH B2056 O 78.5 157.9 86.0 REMARK 620 5 HOH B2059 O 172.4 94.8 85.2 95.3 REMARK 620 6 HOH B2061 O 84.9 99.9 173.0 97.5 100.5 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 D28 B1200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GSH A1200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GSH B1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GSH C1200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GSH D1200 REMARK 900 REMARK 900 RELATED ENTRIES 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: 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: 2VCX RELATED DB: PDB REMARK 900 COMPLEX STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE AT 2.1A. 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 2VD1 A 1 199 UNP O60760 PTGD2_HUMAN 1 199 DBREF 2VD1 B 1 199 UNP O60760 PTGD2_HUMAN 1 199 DBREF 2VD1 C 1 199 UNP O60760 PTGD2_HUMAN 1 199 DBREF 2VD1 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 D28 B1200 24 HET MG B1201 1 HET GSH B1202 20 HET GSH C1200 20 HET GSH D1200 20 HETNAM GSH GLUTATHIONE HETNAM D28 4-{[4-(4-FLUORO-3-METHYLPHENYL)-1,3-THIAZOL-2- HETNAM 2 D28 YL]AMINO}-2-HYDROXYBENZOIC ACID HETNAM MG MAGNESIUM ION FORMUL 5 GSH 4(C10 H17 N3 O6 S) FORMUL 6 D28 C17 H13 F N2 O3 S FORMUL 7 MG MG 2+ FORMUL 11 HOH *349(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 SER A 44 1 7 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 CYS B 101 1 21 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 ALA C 15 LEU C 25 1 11 HELIX 24 24 GLU C 35 ALA C 37 5 3 HELIX 25 25 ASP C 38 SER C 44 1 7 HELIX 26 26 GLN C 63 LYS C 73 1 11 HELIX 27 27 THR C 81 MET C 99 1 19 HELIX 28 28 TYR C 122 GLY C 136 1 15 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 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 PHE D 102 1 22 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 O HOH A2043 MG MG B1201 1555 1555 2.09 LINK O HOH A2046 MG MG B1201 1555 1555 1.89 LINK O HOH A2048 MG MG B1201 1555 1555 2.17 LINK MG MG B1201 O HOH B2056 1555 1555 2.24 LINK MG MG B1201 O HOH B2059 1555 1555 2.28 LINK MG MG B1201 O HOH B2061 1555 1555 2.11 CISPEP 1 ILE A 51 PRO A 52 0 3.44 CISPEP 2 ILE B 51 PRO B 52 0 4.99 CISPEP 3 ILE C 51 PRO C 52 0 2.93 CISPEP 4 ILE D 51 PRO D 52 0 5.30 SITE 1 AC1 11 PHE B 9 MET B 11 GLY B 13 ARG B 14 SITE 2 AC1 11 GLN B 36 ASP B 96 MET B 99 TRP B 104 SITE 3 AC1 11 TYR B 152 GSH B1202 HOH B2104 SITE 1 AC2 6 HOH A2043 HOH A2046 HOH A2048 HOH B2056 SITE 2 AC2 6 HOH B2059 HOH B2061 SITE 1 AC3 12 TYR A 8 ARG A 14 TRP A 39 LYS A 43 SITE 2 AC3 12 GLY A 49 LYS A 50 ILE A 51 GLN A 63 SITE 3 AC3 12 SER A 64 HOH A2023 HOH A2047 ASP B 97 SITE 1 AC4 13 ASP A 97 TYR B 8 ARG B 14 TRP B 39 SITE 2 AC4 13 LYS B 43 LYS B 50 ILE B 51 GLN B 63 SITE 3 AC4 13 SER B 64 D28 B1200 HOH B2010 HOH B2060 SITE 4 AC4 13 HOH B2107 SITE 1 AC5 12 TYR C 8 ARG C 14 TRP C 39 LYS C 43 SITE 2 AC5 12 LYS C 50 ILE C 51 GLN C 63 SER C 64 SITE 3 AC5 12 HOH C2085 HOH C2086 HOH C2087 ASP D 97 SITE 1 AC6 13 ASP C 97 TYR D 8 ARG D 14 TRP D 39 SITE 2 AC6 13 LYS D 43 GLY D 49 LYS D 50 ILE D 51 SITE 3 AC6 13 PRO D 52 GLN D 63 SER D 64 HOH D2020 SITE 4 AC6 13 HOH D2038 CRYST1 123.521 123.521 106.289 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 0.008096 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008096 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009408 0.00000