PDB Short entry for 5AIX HEADER TRANSFERASE 18-FEB-15 5AIX TITLE COMPLEX OF HUMAN HEMATOPOIETIC PROSTAGANDIN D2 SYNTHASE (HH- TITLE 2 PGDS) IN COMPLEX WITH AN ACTIVE SITE INHIBITOR. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE; COMPND 3 CHAIN: A, C, B, D; COMPND 4 SYNONYM: H-PGDS, GST CLASS-SIGMA, GLUTATHIONE S-TRANSFERASE, COMPND 5 GLUTATH IONE-DEPENDENT PGD SYNTHASE, GLUTATHIONE-REQUIRING COMPND 6 PROSTAGLANDIN D SYNTHASE, PROSTAGLANDIN-H2 D-ISOMERASE; COMPND 7 EC: 5.3.99.2, 2.5.1.18; COMPND 8 ENGINEERED: YES 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: 562 KEYWDS TRANSFERASE, PROSTAGLANDIN D2 SYNTHASE, PGDS INHIBITORS, INDOLE, KEYWDS 2 FOCUSED SCREENING, HIT VALIDATION EXPDTA X-RAY DIFFRACTION AUTHOR F.EDFELDT,J.EVENAS,M.LEPISTO,A.WARD,J.PETERSEN,L.WISSLER,M.ROHMAN, AUTHOR 2 U.SIVARS,K.SVENSSON,M.PERRY,I.FEIERBERG,X.ZHOU,T.HANSSON,F.NARJES REVDAT 2 10-JUN-15 5AIX 1 JRNL REVDAT 1 03-JUN-15 5AIX 0 JRNL AUTH F.EDFELDT,J.EVEN,M.LEPISTO,A.WARD,J.PETERSEN,L.WISSLER, JRNL AUTH 2 M.ROHMAN,U.SIVARS,K.SVENSSON,M.PERRY,I.FEIERBERG,X.H.ZHOU, JRNL AUTH 3 T.HANSSON,F.NARJES JRNL TITL IDENTIFICATION OF INDOLE INHIBITORS OF HUMAN HEMATOPOIETIC JRNL TITL 2 PROSTAGLANDIN D2 SYNTHASE (HH-PGDS). JRNL REF BIOORG.MED.CHEM.LETT. V. 25 2496 2015 JRNL REFN ISSN 0960-894X JRNL PMID 25978964 JRNL DOI 10.1016/J.BMCL.2015.04.065 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 96.82 REMARK 3 NUMBER OF REFLECTIONS : 41760 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) : 0.26068 REMARK 3 R VALUE (WORKING SET) : 0.25630 REMARK 3 FREE R VALUE : 0.34295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 2236 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) : 2.100 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.155 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2855 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.374 REMARK 3 BIN FREE R VALUE SET COUNT : 142 REMARK 3 BIN FREE R VALUE : 0.464 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6552 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 98 REMARK 3 SOLVENT ATOMS : 99 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.151 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00 REMARK 3 B22 (A**2) : 0.00 REMARK 3 B33 (A**2) : 0.01 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.374 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.298 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.295 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.561 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.904 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.827 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6822 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9280 ; 1.573 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 788 ; 6.618 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 336 ;38.419 ;24.286 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1160 ;19.502 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;18.870 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1008 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5244 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 3972 ; 0.677 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6460 ; 1.216 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2850 ; 1.825 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2820 ; 2.709 ; 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: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 5AIX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-FEB-15. REMARK 100 THE PDBE ID CODE IS EBI-63086. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 0.873 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : 45383 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.10 REMARK 200 RESOLUTION RANGE LOW (A) : 43.21 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.6 REMARK 200 R MERGE (I) : 0.20 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.30 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.5 REMARK 200 R MERGE FOR SHELL (I) : 1.46 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.50 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: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 61.11400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 61.11400 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.01150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 61.11400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.50575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 61.11400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 79.51725 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 61.11400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.11400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 53.01150 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 61.11400 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 79.51725 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 61.11400 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 26.50575 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.7 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 HIS A 1 REMARK 465 HIS B 1 REMARK 465 HIS C 1 REMARK 465 HIS 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 GLN A 129 OG1 THR A 133 2.11 REMARK 500 NE ARG B 14 O HOH B 2003 2.18 REMARK 500 NH2 ARG D 138 O LEU D 141 2.12 REMARK 500 OG1 THR D 197 O LEU D 199 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O TYR A 134 NZ LYS B 192 7554 2.06 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 PRO A 125 C - N - CA ANGL. DEV. = -9.6 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 MET A 11 -172.72 -173.02 REMARK 500 ARG A 12 -74.79 -97.89 REMARK 500 ASP A 26 60.64 61.14 REMARK 500 ALA A 37 -51.43 -14.06 REMARK 500 LYS A 43 -37.96 -33.44 REMARK 500 GLN A 63 99.24 64.07 REMARK 500 ASN A 74 15.55 81.89 REMARK 500 THR A 75 -168.23 -103.79 REMARK 500 SER A 100 -3.05 -57.14 REMARK 500 LYS A 112 -75.52 -51.57 REMARK 500 LYS A 164 89.90 -150.58 REMARK 500 PHE B 22 -71.66 -40.91 REMARK 500 LEU B 25 35.08 -72.16 REMARK 500 ASP B 26 70.12 22.69 REMARK 500 ASP B 57 83.75 43.95 REMARK 500 GLN B 63 95.75 85.48 REMARK 500 ASN B 80 2.96 -65.15 REMARK 500 PRO B 195 152.47 -49.63 REMARK 500 ASN C 3 67.17 -109.10 REMARK 500 ASN C 10 69.68 -65.35 REMARK 500 ASP C 31 82.71 -66.97 REMARK 500 ASP C 57 46.19 37.24 REMARK 500 GLN C 63 105.05 63.77 REMARK 500 GLU C 73 124.99 -32.69 REMARK 500 ASN C 74 19.17 59.64 REMARK 500 ASN D 10 72.70 -62.58 REMARK 500 ASP D 26 27.80 44.32 REMARK 500 HIS D 32 88.66 -65.25 REMARK 500 TRP D 39 -80.27 -55.16 REMARK 500 LYS D 43 -3.72 -49.19 REMARK 500 GLN D 63 114.89 75.19 REMARK 500 ASN D 74 16.39 83.88 REMARK 500 PRO D 103 82.55 -67.60 REMARK 500 LYS D 108 95.08 -69.87 REMARK 500 PHE D 116 -74.42 -57.83 REMARK 500 THR D 158 -70.06 -53.75 REMARK 500 ASN D 189 -74.23 -43.94 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 A2021 O REMARK 620 2 HOH A2032 O 84.5 REMARK 620 3 HOH A2034 O 87.5 80.3 REMARK 620 4 HOH A2033 O 166.4 83.1 96.0 REMARK 620 5 HOH A2022 O 113.5 160.1 107.6 78.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D1200 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C2019 O REMARK 620 2 HOH C2021 O 99.2 REMARK 620 3 HOH D2006 O 158.5 99.3 REMARK 620 4 HOH D2007 O 89.6 171.1 72.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GSH B1200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GSH C1200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KRX C1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KRX B1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D1200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AIS RELATED DB: PDB REMARK 900 COMPLEX OF HUMAN HEMATOPOIETIC PROSTAGANDIN D2 SYNTHASE ( REMARK 900 HH-PGDS) IN COMPLEX WITH AN ACTIVE SITE INHIBITOR. REMARK 900 RELATED ID: 5AIV RELATED DB: PDB REMARK 900 COMPLEX OF HUMAN HEMATOPOIETIC PROSTAGANDIN D2 SYNTHASE ( REMARK 900 HH-PGDS) IN COMPLEX WITH AN ACTIVE SITE INHIBITOR. DBREF 5AIX A 2 199 UNP O60760 HPGDS_HUMAN 2 199 DBREF 5AIX B 2 199 UNP O60760 HPGDS_HUMAN 2 199 DBREF 5AIX C 2 199 UNP O60760 HPGDS_HUMAN 2 199 DBREF 5AIX D 2 199 UNP O60760 HPGDS_HUMAN 2 199 SEQADV 5AIX HIS A 1 UNP O60760 EXPRESSION TAG SEQADV 5AIX GLU A 73 UNP O60760 LYS 73 CONFLICT SEQADV 5AIX HIS B 1 UNP O60760 EXPRESSION TAG SEQADV 5AIX GLU B 73 UNP O60760 LYS 73 CONFLICT SEQADV 5AIX HIS C 1 UNP O60760 EXPRESSION TAG SEQADV 5AIX GLU C 73 UNP O60760 LYS 73 CONFLICT SEQADV 5AIX HIS D 1 UNP O60760 EXPRESSION TAG SEQADV 5AIX GLU D 73 UNP O60760 LYS 73 CONFLICT SEQRES 1 A 199 HIS 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 GLU 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 HIS 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 GLU 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 HIS 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 GLU 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 HIS 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 GLU 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 B1200 20 HET GSH C1200 20 HET KRX C1201 28 HET KRX B1201 28 HET MG A1200 1 HET MG D1200 1 HETNAM KRX 6-(3-METHOXYPHENYL)-N-[1-(2,2,2- HETNAM 2 KRX TRIFLUOROETHYL)PIPERIDIN-4-YL]PYRIDINE-3- HETNAM 3 KRX CARBOXAMIDE HETNAM GSH GLUTATHIONE HETNAM MG MAGNESIUM ION FORMUL 5 KRX 2(C20 H22 F3 N3 O2) FORMUL 6 GSH 2(C10 H18 N3 O6 S 1+) FORMUL 7 MG 2(MG 2+) FORMUL 8 HOH *99(H2 O) HELIX 1 1 ALA A 15 ASP A 26 1 12 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 GLU A 73 1 11 HELIX 5 5 THR A 81 SER A 100 1 20 HELIX 6 6 LYS A 108 TYR A 122 1 15 HELIX 7 7 TYR A 122 GLY A 136 1 15 HELIX 8 8 THR A 147 LYS A 164 1 18 HELIX 9 9 PRO A 165 ASP A 169 5 5 HELIX 10 10 HIS A 171 ILE A 184 1 14 HELIX 11 11 ILE A 184 ARG A 194 1 11 HELIX 12 12 ALA B 15 LEU B 25 1 11 HELIX 13 13 ASP B 38 SER B 44 1 7 HELIX 14 14 GLN B 63 LEU B 71 1 9 HELIX 15 15 THR B 81 SER B 100 1 20 HELIX 16 16 LYS B 108 TYR B 122 1 15 HELIX 17 17 ASN B 123 GLY B 136 1 14 HELIX 18 18 THR B 147 LYS B 164 1 18 HELIX 19 19 HIS B 171 ALA B 183 1 13 HELIX 20 20 ILE B 184 ARG B 194 1 11 HELIX 21 21 ALA C 15 LEU C 25 1 11 HELIX 22 22 GLU C 35 ALA C 37 5 3 HELIX 23 23 ASP C 38 THR C 45 1 8 HELIX 24 24 GLN C 63 LEU C 71 1 9 HELIX 25 25 THR C 81 SER C 100 1 20 HELIX 26 26 LYS C 108 ASN C 123 1 16 HELIX 27 27 ASN C 123 GLY C 136 1 14 HELIX 28 28 THR C 147 LYS C 164 1 18 HELIX 29 29 HIS C 171 ILE C 184 1 14 HELIX 30 30 ILE C 184 ARG C 194 1 11 HELIX 31 31 ALA D 15 LEU D 25 1 11 HELIX 32 32 GLU D 35 ILE D 42 5 8 HELIX 33 33 GLN D 63 GLU D 73 1 11 HELIX 34 34 THR D 81 CYS D 101 1 21 HELIX 35 35 LYS D 108 GLY D 136 1 29 HELIX 36 36 THR D 147 LYS D 164 1 18 HELIX 37 37 HIS D 171 ALA D 183 1 13 HELIX 38 38 ILE D 184 ARG D 193 1 10 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 THR B 60 HIS B 62 -1 O LEU B 61 N LEU B 54 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 TYR D 29 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 LINK MG MG A1200 O HOH A2021 1555 1555 1.99 LINK MG MG A1200 O HOH A2032 1555 1555 2.47 LINK MG MG A1200 O HOH A2034 1555 1555 2.30 LINK MG MG A1200 O HOH A2033 1555 1555 2.31 LINK MG MG A1200 O HOH A2022 1555 1555 2.21 LINK MG MG D1200 O HOH C2021 1555 1555 1.83 LINK MG MG D1200 O HOH D2006 1555 1555 2.48 LINK MG MG D1200 O HOH D2007 1555 1555 2.05 LINK MG MG D1200 O HOH C2019 1555 1555 2.12 CISPEP 1 ILE A 51 PRO A 52 0 3.91 CISPEP 2 ILE B 51 PRO B 52 0 10.30 CISPEP 3 ILE C 51 PRO C 52 0 7.13 CISPEP 4 ILE D 51 PRO D 52 0 7.91 SITE 1 AC1 12 ASP A 97 TYR B 8 ARG B 14 TRP B 39 SITE 2 AC1 12 LYS B 43 GLY B 49 LYS B 50 ILE B 51 SITE 3 AC1 12 GLN B 63 SER B 64 KRX B1201 HOH B2010 SITE 1 AC2 13 TYR C 8 ARG C 14 TRP C 39 LYS C 43 SITE 2 AC2 13 LYS C 50 ILE C 51 PRO C 52 GLN C 63 SITE 3 AC2 13 SER C 64 KRX C1201 HOH C2008 HOH C2011 SITE 4 AC2 13 ASP D 97 SITE 1 AC3 11 PHE C 9 GLY C 13 ARG C 14 GLN C 36 SITE 2 AC3 11 MET C 99 TRP C 104 TYR C 152 ILE C 155 SITE 3 AC3 11 LEU C 199 GSH C1200 HOH C2023 SITE 1 AC4 11 PHE B 9 MET B 11 GLY B 13 ARG B 14 SITE 2 AC4 11 GLN B 36 MET B 99 TRP B 104 TYR B 152 SITE 3 AC4 11 ILE B 155 LEU B 199 GSH B1200 SITE 1 AC5 6 HOH A2021 HOH A2022 HOH A2032 HOH A2033 SITE 2 AC5 6 HOH A2034 ASP B 93 SITE 1 AC6 4 HOH C2019 HOH C2021 HOH D2006 HOH D2007 CRYST1 122.228 122.228 106.023 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 0.008181 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008181 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009432 0.00000