PDB Short entry for 3VI7 HEADER ISOMERASE/ISOMERASE INHIBITOR 21-SEP-11 3VI7 TITLE HUMAN HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE INHIBITOR COMPLEX TITLE 2 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: H-PGDS, GST CLASS-SIGMA, GLUTATHIONE S-TRANSFERASE, COMPND 5 GLUTATHIONE-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; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HPGDS, GSTS, PGDS, PTGDS2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS SIGMA CLASS GLUTATHIONE S TRANSFERASE(GST), ISOMERASE, GLUTATHIONE S KEYWDS 2 TRANSFERASE, CA BINDING, GSH BINDING, PROSTAGLANDIN H2 BINDING, KEYWDS 3 ISOMERASE-ISOMERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.KADO,T.INOUE REVDAT 2 20-MAR-24 3VI7 1 REMARK SEQADV LINK REVDAT 1 18-APR-12 3VI7 0 JRNL AUTH Y.KADO,K.ARITAKE,N.UODOME,Y.OKANO,N.OKAZAKI,H.MATSUMURA, JRNL AUTH 2 Y.URADE,T.INOUE JRNL TITL HUMAN HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE INHIBITOR JRNL TITL 2 COMPLEX STRUCTURES JRNL REF J.BIOCHEM. V. 151 447 2012 JRNL REFN ISSN 0021-924X JRNL PMID 22418579 JRNL DOI 10.1093/JB/MVS024 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 56092 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2840 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3866 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE SET COUNT : 218 REMARK 3 BIN FREE R VALUE : 0.2870 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 : 184 REMARK 3 SOLVENT ATOMS : 743 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.179 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.106 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6912 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9410 ; 1.891 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 788 ; 5.953 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 328 ;36.973 ;24.146 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1176 ;16.694 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;17.076 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1018 ; 0.153 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5242 ; 0.011 ; 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 ; 1.203 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6460 ; 2.035 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2940 ; 3.312 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2950 ; 5.013 ; 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 : 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3VI7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000095075. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-03 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 : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : FIXED EXIT SI 111 DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56268 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG6000, TRIS-HCL, CACL2, GSH, DTT, REMARK 280 1,4-DIOXANE,, PH 8.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 23.67950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: 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 HOH B 676 O HOH B 767 1.99 REMARK 500 O HOH A 405 O HOH A 540 2.00 REMARK 500 O HOH A 238 O HOH A 492 2.01 REMARK 500 NH2 ARG A 14 OD1 ASP A 96 2.08 REMARK 500 NH1 ARG B 214 O11 GSH B 400 2.09 REMARK 500 O HOH A 746 O HOH A 764 2.10 REMARK 500 ND2 ASN D 770 O HOH D 840 2.11 REMARK 500 O HOH A 654 O HOH A 770 2.15 REMARK 500 OE1 GLU B 255 O HOH B 418 2.16 REMARK 500 OE2 GLU B 284 O HOH B 774 2.16 REMARK 500 NH1 ARG A 138 O HOH A 285 2.17 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 HOH B 846 O HOH C 801 1565 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 8 CD1 TYR A 8 CE1 0.100 REMARK 500 GLU A 30 CB GLU A 30 CG 0.117 REMARK 500 TYR A 122 CD1 TYR A 122 CE1 0.108 REMARK 500 TYR A 122 CE2 TYR A 122 CD2 0.100 REMARK 500 TYR D 629 CD1 TYR D 629 CE1 0.095 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 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 214 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 233 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG C 414 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG C 414 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG C 538 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG C 578 NE - CZ - NH2 ANGL. DEV. = -3.2 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 ASP A 57 51.24 36.67 REMARK 500 GLN A 63 110.11 75.23 REMARK 500 GLN B 263 113.99 71.88 REMARK 500 SER C 444 -25.33 -38.26 REMARK 500 PRO C 447 -38.91 -38.79 REMARK 500 GLN C 463 109.60 75.74 REMARK 500 GLN D 663 110.94 76.58 REMARK 500 TYR D 722 -63.46 -92.99 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 CA D 901 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 239 O REMARK 620 2 HOH A 302 O 81.3 REMARK 620 3 HOH D 255 O 87.1 122.1 REMARK 620 4 ASP D 696 OD2 157.5 114.5 71.0 REMARK 620 5 HOH D 835 O 67.5 145.8 71.5 99.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 902 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 42 O REMARK 620 2 HOH B 462 O 75.8 REMARK 620 3 HOH B 505 O 59.5 67.2 REMARK 620 4 HOH C 165 O 95.1 124.0 61.3 REMARK 620 5 HOH C 336 O 65.8 138.9 103.0 75.2 REMARK 620 6 ASP C 496 OD2 173.4 108.9 117.6 78.4 110.7 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 GSH A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CBD A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GSH B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CBD B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GSH C 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GSH D 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA D 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IYI RELATED DB: PDB REMARK 900 RELATED ID: 1IYH RELATED DB: PDB REMARK 900 RELATED ID: 1V40 RELATED DB: PDB REMARK 900 RELATED ID: 2CVD RELATED DB: PDB REMARK 900 RELATED ID: 3VI5 RELATED DB: PDB DBREF 3VI7 A 2 199 UNP O60760 HPGDS_HUMAN 2 199 DBREF 3VI7 B 202 399 UNP O60760 HPGDS_HUMAN 2 199 DBREF 3VI7 C 402 599 UNP O60760 HPGDS_HUMAN 2 199 DBREF 3VI7 D 602 799 UNP O60760 HPGDS_HUMAN 2 199 SEQADV 3VI7 MET A 144 UNP O60760 ASN 144 ENGINEERED MUTATION SEQADV 3VI7 MET B 344 UNP O60760 ASN 144 ENGINEERED MUTATION SEQADV 3VI7 MET C 544 UNP O60760 ASN 144 ENGINEERED MUTATION SEQADV 3VI7 MET D 744 UNP O60760 ASN 144 ENGINEERED MUTATION SEQRES 1 A 198 PRO ASN TYR LYS LEU THR TYR PHE ASN MET ARG GLY ARG SEQRES 2 A 198 ALA GLU ILE ILE ARG TYR ILE PHE ALA TYR LEU ASP ILE SEQRES 3 A 198 GLN TYR GLU ASP HIS ARG ILE GLU GLN ALA ASP TRP PRO SEQRES 4 A 198 GLU ILE LYS SER THR LEU PRO PHE GLY LYS ILE PRO ILE SEQRES 5 A 198 LEU GLU VAL ASP GLY LEU THR LEU HIS GLN SER LEU ALA SEQRES 6 A 198 ILE ALA ARG TYR LEU THR LYS ASN THR ASP LEU ALA GLY SEQRES 7 A 198 ASN THR GLU MET GLU GLN CYS HIS VAL ASP ALA ILE VAL SEQRES 8 A 198 ASP THR LEU ASP ASP PHE MET SER CYS PHE PRO TRP ALA SEQRES 9 A 198 GLU LYS LYS GLN ASP VAL LYS GLU GLN MET PHE ASN GLU SEQRES 10 A 198 LEU LEU THR TYR ASN ALA PRO HIS LEU MET GLN ASP LEU SEQRES 11 A 198 ASP THR TYR LEU GLY GLY ARG GLU TRP LEU ILE GLY MET SEQRES 12 A 198 SER VAL THR TRP ALA ASP PHE TYR TRP GLU ILE CYS SER SEQRES 13 A 198 THR THR LEU LEU VAL PHE LYS PRO ASP LEU LEU ASP ASN SEQRES 14 A 198 HIS PRO ARG LEU VAL THR LEU ARG LYS LYS VAL GLN ALA SEQRES 15 A 198 ILE PRO ALA VAL ALA ASN TRP ILE LYS ARG ARG PRO GLN SEQRES 16 A 198 THR LYS LEU SEQRES 1 B 198 PRO ASN TYR LYS LEU THR TYR PHE ASN MET ARG GLY ARG SEQRES 2 B 198 ALA GLU ILE ILE ARG TYR ILE PHE ALA TYR LEU ASP ILE SEQRES 3 B 198 GLN TYR GLU ASP HIS ARG ILE GLU GLN ALA ASP TRP PRO SEQRES 4 B 198 GLU ILE LYS SER THR LEU PRO PHE GLY LYS ILE PRO ILE SEQRES 5 B 198 LEU GLU VAL ASP GLY LEU THR LEU HIS GLN SER LEU ALA SEQRES 6 B 198 ILE ALA ARG TYR LEU THR LYS ASN THR ASP LEU ALA GLY SEQRES 7 B 198 ASN THR GLU MET GLU GLN CYS HIS VAL ASP ALA ILE VAL SEQRES 8 B 198 ASP THR LEU ASP ASP PHE MET SER CYS PHE PRO TRP ALA SEQRES 9 B 198 GLU LYS LYS GLN ASP VAL LYS GLU GLN MET PHE ASN GLU SEQRES 10 B 198 LEU LEU THR TYR ASN ALA PRO HIS LEU MET GLN ASP LEU SEQRES 11 B 198 ASP THR TYR LEU GLY GLY ARG GLU TRP LEU ILE GLY MET SEQRES 12 B 198 SER VAL THR TRP ALA ASP PHE TYR TRP GLU ILE CYS SER SEQRES 13 B 198 THR THR LEU LEU VAL PHE LYS PRO ASP LEU LEU ASP ASN SEQRES 14 B 198 HIS PRO ARG LEU VAL THR LEU ARG LYS LYS VAL GLN ALA SEQRES 15 B 198 ILE PRO ALA VAL ALA ASN TRP ILE LYS ARG ARG PRO GLN SEQRES 16 B 198 THR LYS LEU SEQRES 1 C 198 PRO ASN TYR LYS LEU THR TYR PHE ASN MET ARG GLY ARG SEQRES 2 C 198 ALA GLU ILE ILE ARG TYR ILE PHE ALA TYR LEU ASP ILE SEQRES 3 C 198 GLN TYR GLU ASP HIS ARG ILE GLU GLN ALA ASP TRP PRO SEQRES 4 C 198 GLU ILE LYS SER THR LEU PRO PHE GLY LYS ILE PRO ILE SEQRES 5 C 198 LEU GLU VAL ASP GLY LEU THR LEU HIS GLN SER LEU ALA SEQRES 6 C 198 ILE ALA ARG TYR LEU THR LYS ASN THR ASP LEU ALA GLY SEQRES 7 C 198 ASN THR GLU MET GLU GLN CYS HIS VAL ASP ALA ILE VAL SEQRES 8 C 198 ASP THR LEU ASP ASP PHE MET SER CYS PHE PRO TRP ALA SEQRES 9 C 198 GLU LYS LYS GLN ASP VAL LYS GLU GLN MET PHE ASN GLU SEQRES 10 C 198 LEU LEU THR TYR ASN ALA PRO HIS LEU MET GLN ASP LEU SEQRES 11 C 198 ASP THR TYR LEU GLY GLY ARG GLU TRP LEU ILE GLY MET SEQRES 12 C 198 SER VAL THR TRP ALA ASP PHE TYR TRP GLU ILE CYS SER SEQRES 13 C 198 THR THR LEU LEU VAL PHE LYS PRO ASP LEU LEU ASP ASN SEQRES 14 C 198 HIS PRO ARG LEU VAL THR LEU ARG LYS LYS VAL GLN ALA SEQRES 15 C 198 ILE PRO ALA VAL ALA ASN TRP ILE LYS ARG ARG PRO GLN SEQRES 16 C 198 THR LYS LEU SEQRES 1 D 198 PRO ASN TYR LYS LEU THR TYR PHE ASN MET ARG GLY ARG SEQRES 2 D 198 ALA GLU ILE ILE ARG TYR ILE PHE ALA TYR LEU ASP ILE SEQRES 3 D 198 GLN TYR GLU ASP HIS ARG ILE GLU GLN ALA ASP TRP PRO SEQRES 4 D 198 GLU ILE LYS SER THR LEU PRO PHE GLY LYS ILE PRO ILE SEQRES 5 D 198 LEU GLU VAL ASP GLY LEU THR LEU HIS GLN SER LEU ALA SEQRES 6 D 198 ILE ALA ARG TYR LEU THR LYS ASN THR ASP LEU ALA GLY SEQRES 7 D 198 ASN THR GLU MET GLU GLN CYS HIS VAL ASP ALA ILE VAL SEQRES 8 D 198 ASP THR LEU ASP ASP PHE MET SER CYS PHE PRO TRP ALA SEQRES 9 D 198 GLU LYS LYS GLN ASP VAL LYS GLU GLN MET PHE ASN GLU SEQRES 10 D 198 LEU LEU THR TYR ASN ALA PRO HIS LEU MET GLN ASP LEU SEQRES 11 D 198 ASP THR TYR LEU GLY GLY ARG GLU TRP LEU ILE GLY MET SEQRES 12 D 198 SER VAL THR TRP ALA ASP PHE TYR TRP GLU ILE CYS SER SEQRES 13 D 198 THR THR LEU LEU VAL PHE LYS PRO ASP LEU LEU ASP ASN SEQRES 14 D 198 HIS PRO ARG LEU VAL THR LEU ARG LYS LYS VAL GLN ALA SEQRES 15 D 198 ILE PRO ALA VAL ALA ASN TRP ILE LYS ARG ARG PRO GLN SEQRES 16 D 198 THR LYS LEU HET GSH A 200 20 HET CBD A 201 51 HET GSH B 400 20 HET CBD B 401 51 HET GSH C 600 20 HET CA C 902 1 HET GSH D 800 20 HET CA D 901 1 HETNAM GSH GLUTATHIONE HETNAM CBD CIBACRON BLUE HETNAM CA CALCIUM ION FORMUL 5 GSH 4(C10 H17 N3 O6 S) FORMUL 6 CBD 2(C29 H20 CL N7 O11 S3) FORMUL 10 CA 2(CA 2+) FORMUL 13 HOH *743(H2 O) HELIX 1 1 ARG A 12 ARG A 14 5 3 HELIX 2 2 ALA A 15 LEU A 25 1 11 HELIX 3 3 GLU A 35 ALA A 37 5 3 HELIX 4 4 ASP A 38 SER A 44 1 7 HELIX 5 5 GLN A 63 LYS A 73 1 11 HELIX 6 6 THR A 81 SER A 100 1 20 HELIX 7 7 LYS A 108 ASN A 123 1 16 HELIX 8 8 ASN A 123 GLY A 136 1 14 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 212 ARG B 214 5 3 HELIX 13 13 ALA B 215 LEU B 225 1 11 HELIX 14 14 GLU B 235 ALA B 237 5 3 HELIX 15 15 ASP B 238 SER B 244 1 7 HELIX 16 16 GLN B 263 LYS B 273 1 11 HELIX 17 17 THR B 281 PHE B 302 1 22 HELIX 18 18 LYS B 308 ASN B 323 1 16 HELIX 19 19 ASN B 323 GLY B 336 1 14 HELIX 20 20 THR B 347 LYS B 364 1 18 HELIX 21 21 HIS B 371 ILE B 384 1 14 HELIX 22 22 ILE B 384 ARG B 394 1 11 HELIX 23 23 ARG C 412 ARG C 414 5 3 HELIX 24 24 ALA C 415 LEU C 425 1 11 HELIX 25 25 GLU C 435 ALA C 437 5 3 HELIX 26 26 ASP C 438 SER C 444 1 7 HELIX 27 27 GLN C 463 LYS C 473 1 11 HELIX 28 28 THR C 481 PHE C 502 1 22 HELIX 29 29 LYS C 508 TYR C 522 1 15 HELIX 30 30 TYR C 522 GLY C 536 1 15 HELIX 31 31 THR C 547 LYS C 564 1 18 HELIX 32 32 HIS C 571 ILE C 584 1 14 HELIX 33 33 ILE C 584 ARG C 594 1 11 HELIX 34 34 ALA D 615 ASP D 626 1 12 HELIX 35 35 GLU D 635 ALA D 637 5 3 HELIX 36 36 ASP D 638 SER D 644 1 7 HELIX 37 37 GLN D 663 LYS D 673 1 11 HELIX 38 38 THR D 681 PHE D 702 1 22 HELIX 39 39 LYS D 708 TYR D 722 1 15 HELIX 40 40 TYR D 722 GLY D 736 1 15 HELIX 41 41 THR D 747 LYS D 764 1 18 HELIX 42 42 HIS D 771 ILE D 784 1 14 HELIX 43 43 ILE D 784 ARG D 794 1 11 SHEET 1 A 4 GLU A 30 ILE A 34 0 SHEET 2 A 4 TYR A 4 PHE A 9 1 N LEU A 6 O GLU A 30 SHEET 3 A 4 ILE A 53 VAL A 56 -1 O GLU A 55 N LYS A 5 SHEET 4 A 4 LEU A 59 HIS A 62 -1 O LEU A 59 N VAL A 56 SHEET 1 B 4 GLU B 230 ILE B 234 0 SHEET 2 B 4 TYR B 204 PHE B 209 1 N LEU B 206 O GLU B 230 SHEET 3 B 4 ILE B 253 VAL B 256 -1 O GLU B 255 N LYS B 205 SHEET 4 B 4 LEU B 259 HIS B 262 -1 O LEU B 259 N VAL B 256 SHEET 1 C 4 GLU C 430 ILE C 434 0 SHEET 2 C 4 TYR C 404 PHE C 409 1 N TYR C 404 O GLU C 430 SHEET 3 C 4 ILE C 453 VAL C 456 -1 O GLU C 455 N LYS C 405 SHEET 4 C 4 LEU C 459 HIS C 462 -1 O LEU C 461 N LEU C 454 SHEET 1 D 4 GLU D 630 ILE D 634 0 SHEET 2 D 4 TYR D 604 PHE D 609 1 N TYR D 608 O ILE D 634 SHEET 3 D 4 ILE D 653 VAL D 656 -1 O GLU D 655 N LYS D 605 SHEET 4 D 4 LEU D 659 HIS D 662 -1 O LEU D 659 N VAL D 656 LINK O HOH A 239 CA CA D 901 1555 1555 2.04 LINK O HOH A 302 CA CA D 901 1555 1555 2.45 LINK O HOH B 42 CA CA C 902 1555 1555 1.92 LINK O HOH B 462 CA CA C 902 1555 1555 2.59 LINK O HOH B 505 CA CA C 902 1555 1555 2.86 LINK O HOH C 165 CA CA C 902 1555 1555 2.57 LINK O HOH C 336 CA CA C 902 1555 1555 2.57 LINK OD2 ASP C 496 CA CA C 902 1555 1555 2.81 LINK O HOH D 255 CA CA D 901 1555 1555 2.69 LINK OD2 ASP D 696 CA CA D 901 1555 1555 2.74 LINK O HOH D 835 CA CA D 901 1555 1555 2.49 CISPEP 1 ILE A 51 PRO A 52 0 6.17 CISPEP 2 ILE B 251 PRO B 252 0 11.55 CISPEP 3 ILE C 451 PRO C 452 0 9.90 CISPEP 4 ILE D 651 PRO D 652 0 6.98 SITE 1 AC1 12 TYR A 8 ARG A 14 TRP A 39 LYS A 50 SITE 2 AC1 12 ILE A 51 PRO A 52 GLN A 63 SER A 64 SITE 3 AC1 12 CBD A 201 HOH A 207 HOH A 662 ASP D 697 SITE 1 AC2 17 GLY A 13 ARG A 14 MET A 99 TRP A 104 SITE 2 AC2 17 ALA A 105 GLU A 106 LYS A 107 TYR A 152 SITE 3 AC2 17 CYS A 156 LYS A 198 LEU A 199 GSH A 200 SITE 4 AC2 17 HOH A 203 HOH A 235 HOH A 288 HOH A 418 SITE 5 AC2 17 HOH A 653 SITE 1 AC3 15 HOH B 71 TYR B 208 ARG B 214 TRP B 239 SITE 2 AC3 15 LYS B 243 LYS B 250 ILE B 251 PRO B 252 SITE 3 AC3 15 GLN B 263 SER B 264 CBD B 401 HOH B 422 SITE 4 AC3 15 HOH B 448 HOH B 850 ASP C 497 SITE 1 AC4 19 HOH B 37 PHE B 209 GLY B 213 ARG B 214 SITE 2 AC4 19 ASP B 296 MET B 299 SER B 300 TRP B 304 SITE 3 AC4 19 ALA B 305 GLU B 306 LYS B 312 TYR B 352 SITE 4 AC4 19 CYS B 356 LYS B 398 LEU B 399 GSH B 400 SITE 5 AC4 19 HOH B 415 HOH B 679 HOH B 868 SITE 1 AC5 15 ASP B 297 HOH C 103 HOH C 282 HOH C 296 SITE 2 AC5 15 HOH C 309 TYR C 408 ARG C 414 TRP C 439 SITE 3 AC5 15 LYS C 443 LYS C 450 ILE C 451 PRO C 452 SITE 4 AC5 15 GLN C 463 SER C 464 HOH C 758 SITE 1 AC6 6 HOH B 42 HOH B 462 HOH B 505 HOH C 165 SITE 2 AC6 6 HOH C 336 ASP C 496 SITE 1 AC7 13 ASP A 97 HOH D 156 TYR D 608 ARG D 614 SITE 2 AC7 13 TRP D 639 LYS D 643 GLY D 649 LYS D 650 SITE 3 AC7 13 ILE D 651 PRO D 652 GLN D 663 SER D 664 SITE 4 AC7 13 HOH D 832 SITE 1 AC8 5 HOH A 239 HOH A 302 HOH D 255 ASP D 696 SITE 2 AC8 5 HOH D 835 CRYST1 49.043 47.359 184.941 90.00 97.41 90.00 P 1 21 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.020390 0.000000 0.002653 0.00000 SCALE2 0.000000 0.021115 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005453 0.00000