HEADER ISOMERASE/ISOMERASE INHIBITOR 21-SEP-11 3VI5 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 3VI5 1 REMARK SEQADV LINK REVDAT 1 18-APR-12 3VI5 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) : 33.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 51115 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2735 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) : 3606 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.2330 REMARK 3 BIN FREE R VALUE SET COUNT : 182 REMARK 3 BIN FREE R VALUE : 0.2710 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 : 112 REMARK 3 SOLVENT ATOMS : 699 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 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): 0.194 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.126 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.475 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6837 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9303 ; 1.799 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 788 ; 5.993 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 328 ;36.789 ;24.146 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1176 ;16.748 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;16.672 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1012 ; 0.133 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5174 ; 0.010 ; 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 ; 1.192 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6460 ; 2.023 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2865 ; 3.272 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2843 ; 5.076 ; 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 3VI5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000095073. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-01 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 : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : ROTATED-INCLINED DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD PX210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53869 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 35.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 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 (%) : 91.6 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 (%): 45.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, TRIS-HCL, DTT, GSH, 1,4 REMARK 280 -DIOXANE, PH 8.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 3700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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: 3380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 C 114 O HOH C 610 2.12 REMARK 500 O HOH A 422 O HOH A 657 2.18 REMARK 500 O HOH C 146 O HOH C 652 2.19 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 GLU D 718 CB GLU D 718 CG 0.118 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 69 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 214 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 214 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG C 414 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG D 614 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 LEU D 720 CB - CG - CD1 ANGL. DEV. = 10.4 DEGREES REMARK 500 ARG D 738 NE - CZ - NH1 ANGL. DEV. = -3.4 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 TRP A 39 -71.63 -64.84 REMARK 500 GLN A 63 115.85 66.26 REMARK 500 GLU A 106 124.16 -38.05 REMARK 500 ASP A 110 -17.16 167.86 REMARK 500 LYS A 164 76.81 -152.07 REMARK 500 GLN B 263 114.42 71.50 REMARK 500 PRO B 303 92.60 -69.32 REMARK 500 GLN C 463 111.18 78.42 REMARK 500 SER D 644 -5.55 -58.82 REMARK 500 ASP D 657 52.36 38.94 REMARK 500 GLN D 663 110.31 73.18 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 900 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 470 O REMARK 620 2 HOH A 640 O 56.4 REMARK 620 3 HOH A 659 O 98.9 51.0 REMARK 620 4 HOH D 278 O 104.5 136.2 103.5 REMARK 620 5 HOH D 509 O 52.8 67.2 115.3 136.6 REMARK 620 6 ASP D 696 OD2 121.0 153.8 140.0 69.6 90.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 901 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 421 O REMARK 620 2 HOH B 426 O 89.3 REMARK 620 3 HOH B 584 O 61.6 113.3 REMARK 620 4 ASP C 496 OD2 114.8 76.4 168.9 REMARK 620 5 HOH C 619 O 101.4 158.3 58.2 114.7 REMARK 620 6 HOH C 644 O 51.9 126.5 82.1 87.7 74.1 REMARK 620 7 HOH C 690 O 131.2 84.1 76.9 110.4 74.6 148.2 REMARK 620 N 1 2 3 4 5 6 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 GSH B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE M4M C 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA D 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE M4M D 804 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: 3VI7 RELATED DB: PDB DBREF 3VI5 A 2 199 UNP O60760 HPGDS_HUMAN 2 199 DBREF 3VI5 B 202 399 UNP O60760 HPGDS_HUMAN 2 199 DBREF 3VI5 C 402 599 UNP O60760 HPGDS_HUMAN 2 199 DBREF 3VI5 D 602 799 UNP O60760 HPGDS_HUMAN 2 199 SEQADV 3VI5 MET A 144 UNP O60760 ASN 144 ENGINEERED MUTATION SEQADV 3VI5 MET B 344 UNP O60760 ASN 144 ENGINEERED MUTATION SEQADV 3VI5 MET C 544 UNP O60760 ASN 144 ENGINEERED MUTATION SEQADV 3VI5 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 GSH B 400 20 HET CA C 901 1 HET M4M C 803 32 HET GOL D1001 6 HET CA D 900 1 HET M4M D 804 32 HETNAM GSH GLUTATHIONE HETNAM CA CALCIUM ION HETNAM M4M 1-AMINO-9,10-DIOXO-4-[(4-SULFAMOYLPHENYL)AMINO]-9,10- HETNAM 2 M4M DIHYDROANTHRACENE-2-SULFONIC ACID HETNAM GOL GLYCEROL HETSYN M4M 1-AMINO-4-(4-AMINOSULFONYL)PHENYLAMINO-ANTHRAQUINONE-2- HETSYN 2 M4M SULFONIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GSH 2(C10 H17 N3 O6 S) FORMUL 7 CA 2(CA 2+) FORMUL 8 M4M 2(C20 H15 N3 O7 S2) FORMUL 9 GOL C3 H8 O3 FORMUL 12 HOH *699(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 LYS A 73 1 11 HELIX 5 5 THR A 81 PHE A 102 1 22 HELIX 6 6 VAL A 111 ASN A 123 1 13 HELIX 7 7 ASN A 123 GLY A 136 1 14 HELIX 8 8 THR A 147 LYS A 164 1 18 HELIX 9 9 HIS A 171 ILE A 184 1 14 HELIX 10 10 ILE A 184 ARG A 194 1 11 HELIX 11 11 ALA B 215 LEU B 225 1 11 HELIX 12 12 GLU B 235 ALA B 237 5 3 HELIX 13 13 ASP B 238 SER B 244 1 7 HELIX 14 14 GLN B 263 LYS B 273 1 11 HELIX 15 15 THR B 281 PHE B 302 1 22 HELIX 16 16 ASP B 310 TYR B 322 1 13 HELIX 17 17 TYR B 322 GLY B 336 1 15 HELIX 18 18 THR B 347 LYS B 364 1 18 HELIX 19 19 HIS B 371 ALA B 383 1 13 HELIX 20 20 ILE B 384 ARG B 394 1 11 HELIX 21 21 ARG C 412 ARG C 414 5 3 HELIX 22 22 ALA C 415 ASP C 426 1 12 HELIX 23 23 GLU C 435 ALA C 437 5 3 HELIX 24 24 ASP C 438 SER C 444 1 7 HELIX 25 25 GLN C 463 LYS C 473 1 11 HELIX 26 26 THR C 481 PHE C 502 1 22 HELIX 27 27 LYS C 508 ASN C 523 1 16 HELIX 28 28 ASN C 523 GLY C 536 1 14 HELIX 29 29 THR C 547 LYS C 564 1 18 HELIX 30 30 HIS C 571 ILE C 584 1 14 HELIX 31 31 ILE C 584 ARG C 594 1 11 HELIX 32 32 ARG D 612 ARG D 614 5 3 HELIX 33 33 ALA D 615 ASP D 626 1 12 HELIX 34 34 GLU D 635 ALA D 637 5 3 HELIX 35 35 ASP D 638 SER D 644 1 7 HELIX 36 36 GLN D 663 LYS D 673 1 11 HELIX 37 37 THR D 681 PHE D 702 1 22 HELIX 38 38 LYS D 708 ASN D 723 1 16 HELIX 39 39 ASN D 723 GLY D 736 1 14 HELIX 40 40 THR D 747 LYS D 764 1 18 HELIX 41 41 HIS D 771 ILE D 784 1 14 HELIX 42 42 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 TYR A 4 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 61 N LEU A 54 SHEET 1 B 4 GLU B 230 ILE B 234 0 SHEET 2 B 4 TYR B 204 PHE B 209 1 N TYR B 204 O GLU B 230 SHEET 3 B 4 ILE B 253 VAL B 256 -1 O ILE B 253 N THR B 207 SHEET 4 B 4 LEU B 259 HIS B 262 -1 O LEU B 261 N LEU B 254 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 408 O ILE C 434 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 459 N VAL C 456 SHEET 1 D 4 GLU D 630 ILE D 634 0 SHEET 2 D 4 TYR D 604 PHE D 609 1 N LEU D 606 O GLU D 630 SHEET 3 D 4 ILE D 653 VAL D 656 -1 O ILE D 653 N THR D 607 SHEET 4 D 4 LEU D 659 HIS D 662 -1 O LEU D 659 N VAL D 656 LINK O HOH A 470 CA CA D 900 1555 1555 2.88 LINK O HOH A 640 CA CA D 900 1555 1555 2.10 LINK O HOH A 659 CA CA D 900 1555 1555 3.11 LINK O HOH B 421 CA CA C 901 1555 1555 2.96 LINK O HOH B 426 CA CA C 901 1555 1555 2.50 LINK O HOH B 584 CA CA C 901 1555 1555 2.15 LINK OD2 ASP C 496 CA CA C 901 1555 1555 2.77 LINK O HOH C 619 CA CA C 901 1555 1555 2.51 LINK O HOH C 644 CA CA C 901 1555 1555 2.79 LINK O HOH C 690 CA CA C 901 1555 1555 2.55 LINK O HOH D 278 CA CA D 900 1555 1555 2.55 LINK O HOH D 509 CA CA D 900 1555 1555 2.84 LINK OD2 ASP D 696 CA CA D 900 1555 1555 2.83 CISPEP 1 ILE A 51 PRO A 52 0 8.14 CISPEP 2 ILE B 251 PRO B 252 0 4.10 CISPEP 3 ILE C 451 PRO C 452 0 8.69 CISPEP 4 ILE D 651 PRO D 652 0 9.47 SITE 1 AC1 12 TYR A 8 ARG A 14 TRP A 39 LYS A 43 SITE 2 AC1 12 GLY A 49 LYS A 50 ILE A 51 PRO A 52 SITE 3 AC1 12 GLN A 63 SER A 64 HOH A 205 ASP D 697 SITE 1 AC2 10 HOH B 78 TYR B 208 ARG B 214 TRP B 239 SITE 2 AC2 10 LYS B 243 LYS B 250 ILE B 251 GLN B 263 SITE 3 AC2 10 SER B 264 ASP C 497 SITE 1 AC3 7 HOH B 421 HOH B 426 HOH B 584 ASP C 496 SITE 2 AC3 7 HOH C 619 HOH C 644 HOH C 690 SITE 1 AC4 11 HOH C 68 HOH C 84 MET C 411 GLY C 413 SITE 2 AC4 11 ARG C 414 LYS C 450 MET C 499 TRP C 504 SITE 3 AC4 11 TYR C 552 HOH C 673 HOH C 738 SITE 1 AC5 6 GLN C 428 TYR C 429 HOH C 667 HOH D 30 SITE 2 AC5 6 HOH D 77 THR D 797 SITE 1 AC6 5 HOH A 470 HOH A 640 HOH D 278 HOH D 509 SITE 2 AC6 5 ASP D 696 SITE 1 AC7 9 HOH D 62 GLY D 613 ARG D 614 LYS D 650 SITE 2 AC7 9 MET D 699 TRP D 704 TYR D 752 HOH D 832 SITE 3 AC7 9 HOH D 834 CRYST1 47.277 48.986 91.919 95.80 90.99 90.14 P 1 4 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 0.021152 0.000052 0.000373 0.00000 SCALE2 0.000000 0.020414 0.002075 0.00000 SCALE3 0.000000 0.000000 0.010937 0.00000