HEADER TRANSFERASE/TRANSFERASE INHIBITOR 30-NOV-17 5YWX TITLE CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE IN COMPLEX TITLE 2 WITH F092 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 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 KEYWDS PROSTAGLANDIN, SYNTHASE, INHIBITOR, TRANSFERASE, TRANSFERASE- KEYWDS 2 TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.KAMO,N.FURUBAYASHI,K.INAKA,K.ARITAKE,A.OMURA,A.TANAKA REVDAT 3 22-NOV-23 5YWX 1 LINK REVDAT 2 12-SEP-18 5YWX 1 JRNL REVDAT 1 05-SEP-18 5YWX 0 JRNL AUTH D.TAKAYA,K.INAKA,A.OMURA,K.TAKENUKI,M.KAWANISHI,Y.YABUKI, JRNL AUTH 2 Y.NAKAGAWA,K.TSUGANEZAWA,N.OGAWA,C.WATANABE,T.HONMA, JRNL AUTH 3 K.ARITAKE,Y.URADE,M.SHIROUZU,A.TANAKA JRNL TITL CHARACTERIZATION OF CRYSTAL WATER MOLECULES IN A JRNL TITL 2 HIGH-AFFINITY INHIBITOR AND HEMATOPOIETIC PROSTAGLANDIN D JRNL TITL 3 SYNTHASE COMPLEX BY INTERACTION ENERGY STUDIES. JRNL REF BIOORG. MED. CHEM. V. 26 4726 2018 JRNL REFN ESSN 1464-3391 JRNL PMID 30121213 JRNL DOI 10.1016/J.BMC.2018.08.014 REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 75464 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) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3992 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) : 1.74 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5481 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE SET COUNT : 271 REMARK 3 BIN FREE R VALUE : 0.3170 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 : 208 REMARK 3 SOLVENT ATOMS : 583 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.48000 REMARK 3 B22 (A**2) : 0.54000 REMARK 3 B33 (A**2) : -0.06000 REMARK 3 B12 (A**2) : 0.04000 REMARK 3 B13 (A**2) : -0.09000 REMARK 3 B23 (A**2) : 0.01000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.145 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.141 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.098 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.980 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6935 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6526 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9419 ; 1.470 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14998 ; 0.807 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 788 ; 5.779 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 332 ;35.458 ;24.217 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1168 ;13.881 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;12.288 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1019 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7724 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1656 ; 0.002 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5YWX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300006046. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : ROTATED-INCLINED DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR , SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.26 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 79469 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 47.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.60900 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: MOLREP 11.0.05 REMARK 200 STARTING MODEL: 2CVD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PEG6000, 5 MM DTT, 2 MM MGCL2, 2 REMARK 280 MM GLUTATHIONE, 2% DIOXANE, 50 MM TRIS-HCL, PH 8.5, LIQUID REMARK 280 DIFFUSION, TEMPERATURE 293.0K 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: 4530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 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 D 487 O HOH D 502 2.00 REMARK 500 O HOH A 471 O HOH A 557 2.08 REMARK 500 OE2 GLU D 55 O HOH D 401 2.12 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 33 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP C 93 CB - CG - OD2 ANGL. DEV. = 5.5 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 ARG A 12 -71.43 -63.69 REMARK 500 ASP A 57 49.53 38.51 REMARK 500 GLN A 63 107.64 74.07 REMARK 500 ARG B 12 -70.48 -68.64 REMARK 500 GLN B 63 111.52 76.65 REMARK 500 GLU B 106 120.87 -23.10 REMARK 500 LYS B 108 105.12 -53.90 REMARK 500 GLN C 63 112.62 80.52 REMARK 500 LYS C 108 91.75 -56.68 REMARK 500 LYS C 112 -60.95 -92.68 REMARK 500 GLN D 63 108.44 74.76 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 B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 456 O REMARK 620 2 HOH A 488 O 88.8 REMARK 620 3 HOH A 529 O 84.7 86.9 REMARK 620 4 HOH B 304 O 87.1 83.8 167.7 REMARK 620 5 HOH B 322 O 95.4 166.6 80.9 109.0 REMARK 620 6 HOH B 329 O 170.8 82.1 93.1 93.6 93.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 322 O REMARK 620 2 HOH C 329 O 95.8 REMARK 620 3 HOH C 334 O 89.2 102.7 REMARK 620 4 HOH D 452 O 170.8 78.7 99.3 REMARK 620 5 HOH D 483 O 91.8 95.7 161.4 81.5 REMARK 620 6 HOH D 485 O 98.1 165.5 81.8 87.0 79.6 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 93C A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GSH B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 93C B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GSH C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 93C C 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GSH D 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 93C D 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 303 DBREF 5YWX A 2 199 UNP O60760 HPGDS_HUMAN 2 199 DBREF 5YWX B 2 199 UNP O60760 HPGDS_HUMAN 2 199 DBREF 5YWX C 2 199 UNP O60760 HPGDS_HUMAN 2 199 DBREF 5YWX D 2 199 UNP O60760 HPGDS_HUMAN 2 199 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 ASN 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 ASN 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 ASN 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 ASN 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 301 20 HET 93C A 302 27 HET GOL A 303 6 HET GOL A 304 6 HET MG B 201 1 HET GSH B 202 20 HET 93C B 203 27 HET MG C 201 1 HET GSH C 202 20 HET 93C C 203 27 HET GSH D 301 20 HET 93C D 302 27 HET GOL D 303 6 HETNAM GSH GLUTATHIONE HETNAM 93C N-[4-(2-OXOPYRROLIDIN-1-YL)PHENYL]-2-(PYRIDIN-2-YL) HETNAM 2 93C PYRIMIDINE-5-CARBOXAMIDE HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GSH 4(C10 H17 N3 O6 S) FORMUL 6 93C 4(C20 H17 N5 O2) FORMUL 7 GOL 3(C3 H8 O3) FORMUL 9 MG 2(MG 2+) FORMUL 18 HOH *583(H2 O) HELIX 1 AA1 ARG A 12 ARG A 14 5 3 HELIX 2 AA2 ALA A 15 LEU A 25 1 11 HELIX 3 AA3 GLU A 35 ALA A 37 5 3 HELIX 4 AA4 ASP A 38 SER A 44 1 7 HELIX 5 AA5 GLN A 63 LYS A 73 1 11 HELIX 6 AA6 THR A 81 CYS A 101 1 21 HELIX 7 AA7 LYS A 108 ASN A 123 1 16 HELIX 8 AA8 ASN A 123 GLY A 136 1 14 HELIX 9 AA9 THR A 147 LYS A 164 1 18 HELIX 10 AB1 HIS A 171 ILE A 184 1 14 HELIX 11 AB2 ILE A 184 ARG A 194 1 11 HELIX 12 AB3 ALA B 15 ASP B 26 1 12 HELIX 13 AB4 GLU B 35 ALA B 37 5 3 HELIX 14 AB5 ASP B 38 LEU B 46 1 9 HELIX 15 AB6 GLN B 63 LYS B 73 1 11 HELIX 16 AB7 THR B 81 SER B 100 1 20 HELIX 17 AB8 ASP B 110 TYR B 122 1 13 HELIX 18 AB9 ASN B 123 GLY B 136 1 14 HELIX 19 AC1 THR B 147 LYS B 164 1 18 HELIX 20 AC2 HIS B 171 ILE B 184 1 14 HELIX 21 AC3 ILE B 184 ARG B 194 1 11 HELIX 22 AC4 ALA C 15 LEU C 25 1 11 HELIX 23 AC5 ASP C 38 SER C 44 1 7 HELIX 24 AC6 GLN C 63 LYS C 73 1 11 HELIX 25 AC7 THR C 81 SER C 100 1 20 HELIX 26 AC8 VAL C 111 ASN C 123 1 13 HELIX 27 AC9 ASN C 123 GLY C 136 1 14 HELIX 28 AD1 THR C 147 LYS C 164 1 18 HELIX 29 AD2 HIS C 171 ALA C 183 1 13 HELIX 30 AD3 ILE C 184 ARG C 194 1 11 HELIX 31 AD4 ARG D 12 ARG D 14 5 3 HELIX 32 AD5 ALA D 15 ASP D 26 1 12 HELIX 33 AD6 GLU D 35 ALA D 37 5 3 HELIX 34 AD7 ASP D 38 SER D 44 1 7 HELIX 35 AD8 GLN D 63 LYS D 73 1 11 HELIX 36 AD9 THR D 81 SER D 100 1 20 HELIX 37 AE1 LYS D 108 ASN D 123 1 16 HELIX 38 AE2 ASN D 123 GLY D 136 1 14 HELIX 39 AE3 THR D 147 LYS D 164 1 18 HELIX 40 AE4 HIS D 171 ILE D 184 1 14 HELIX 41 AE5 ILE D 184 ARG D 194 1 11 SHEET 1 AA1 4 GLU A 30 ILE A 34 0 SHEET 2 AA1 4 TYR A 4 PHE A 9 1 N LEU A 6 O GLU A 30 SHEET 3 AA1 4 ILE A 53 VAL A 56 -1 O GLU A 55 N LYS A 5 SHEET 4 AA1 4 LEU A 59 HIS A 62 -1 O LEU A 61 N LEU A 54 SHEET 1 AA2 4 GLU B 30 ILE B 34 0 SHEET 2 AA2 4 TYR B 4 PHE B 9 1 N TYR B 4 O GLU B 30 SHEET 3 AA2 4 ILE B 53 VAL B 56 -1 O GLU B 55 N LYS B 5 SHEET 4 AA2 4 LEU B 59 HIS B 62 -1 O LEU B 59 N VAL B 56 SHEET 1 AA3 4 GLU C 30 ILE C 34 0 SHEET 2 AA3 4 TYR C 4 PHE C 9 1 N LEU C 6 O GLU C 30 SHEET 3 AA3 4 ILE C 53 VAL C 56 -1 O ILE C 53 N THR C 7 SHEET 4 AA3 4 LEU C 59 HIS C 62 -1 O LEU C 59 N VAL C 56 SHEET 1 AA4 4 GLU D 30 ILE D 34 0 SHEET 2 AA4 4 TYR D 4 PHE D 9 1 N TYR D 4 O GLU D 30 SHEET 3 AA4 4 ILE D 53 VAL D 56 -1 O GLU D 55 N LYS D 5 SHEET 4 AA4 4 LEU D 59 HIS D 62 -1 O LEU D 61 N LEU D 54 LINK O HOH A 456 MG MG B 201 1555 1555 2.18 LINK O HOH A 488 MG MG B 201 1555 1555 2.04 LINK O HOH A 529 MG MG B 201 1555 1555 2.24 LINK MG MG B 201 O HOH B 304 1555 1555 1.92 LINK MG MG B 201 O HOH B 322 1555 1555 1.98 LINK MG MG B 201 O HOH B 329 1555 1555 2.23 LINK MG MG C 201 O HOH C 322 1555 1555 2.05 LINK MG MG C 201 O HOH C 329 1555 1555 2.06 LINK MG MG C 201 O HOH C 334 1555 1555 2.01 LINK MG MG C 201 O HOH D 452 1555 1555 2.16 LINK MG MG C 201 O HOH D 483 1555 1555 2.33 LINK MG MG C 201 O HOH D 485 1555 1555 2.14 CISPEP 1 ILE A 51 PRO A 52 0 10.98 CISPEP 2 ILE B 51 PRO B 52 0 5.54 CISPEP 3 ILE C 51 PRO C 52 0 9.13 CISPEP 4 ILE D 51 PRO D 52 0 6.93 SITE 1 AC1 14 TYR A 8 ARG A 14 TRP A 39 LYS A 50 SITE 2 AC1 14 ILE A 51 PRO A 52 GLN A 63 SER A 64 SITE 3 AC1 14 93C A 302 HOH A 461 HOH A 468 HOH A 502 SITE 4 AC1 14 HOH A 514 ASP B 97 SITE 1 AC2 14 MET A 11 GLY A 13 ARG A 14 GLN A 36 SITE 2 AC2 14 MET A 99 TRP A 104 ALA A 105 TYR A 152 SITE 3 AC2 14 LEU A 199 GSH A 301 HOH A 421 HOH A 442 SITE 4 AC2 14 HOH A 503 GLY B 58 SITE 1 AC3 9 GLN A 196 THR A 197 HOH A 415 HOH A 444 SITE 2 AC3 9 HOH A 505 HOH A 542 GLN D 28 TYR D 29 SITE 3 AC3 9 GOL D 303 SITE 1 AC4 7 GLN A 28 TYR A 29 HOH A 428 HOH A 520 SITE 2 AC4 7 GLN D 196 THR D 197 LYS D 198 SITE 1 AC5 6 HOH A 456 HOH A 488 HOH A 529 HOH B 304 SITE 2 AC5 6 HOH B 322 HOH B 329 SITE 1 AC6 13 ASP A 97 TYR B 8 ARG B 14 TRP B 39 SITE 2 AC6 13 LYS B 43 GLY B 49 LYS B 50 ILE B 51 SITE 3 AC6 13 PRO B 52 GLN B 63 SER B 64 HOH B 328 SITE 4 AC6 13 HOH B 350 SITE 1 AC7 8 GLY B 13 ARG B 14 GLN B 36 MET B 99 SITE 2 AC7 8 TRP B 104 ALA B 105 TYR B 152 HOH B 321 SITE 1 AC8 6 HOH C 322 HOH C 329 HOH C 334 HOH D 452 SITE 2 AC8 6 HOH D 483 HOH D 485 SITE 1 AC9 13 TYR C 8 ARG C 14 TRP C 39 LYS C 43 SITE 2 AC9 13 LYS C 50 ILE C 51 PRO C 52 GLN C 63 SITE 3 AC9 13 SER C 64 93C C 203 HOH C 325 HOH C 336 SITE 4 AC9 13 ASP D 97 SITE 1 AD1 11 MET C 11 GLY C 13 ARG C 14 GLN C 36 SITE 2 AD1 11 MET C 99 TRP C 104 ALA C 105 TYR C 152 SITE 3 AD1 11 LEU C 199 GSH C 202 HOH C 310 SITE 1 AD2 12 ASP C 97 TYR D 8 ARG D 14 TRP D 39 SITE 2 AD2 12 LYS D 50 ILE D 51 PRO D 52 GLN D 63 SITE 3 AD2 12 SER D 64 93C D 302 HOH D 430 HOH D 459 SITE 1 AD3 13 LEU C 59 MET D 11 GLY D 13 ARG D 14 SITE 2 AD3 13 GLN D 36 MET D 99 TRP D 104 ALA D 105 SITE 3 AD3 13 TYR D 152 LEU D 199 GSH D 301 HOH D 416 SITE 4 AD3 13 HOH D 446 SITE 1 AD4 7 LYS A 198 GOL A 303 GLN D 28 TYR D 29 SITE 2 AD4 7 HOH D 415 HOH D 436 HOH D 540 CRYST1 47.040 48.170 92.110 98.97 92.34 90.01 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 0.021259 0.000004 0.000880 0.00000 SCALE2 0.000000 0.020760 0.003280 0.00000 SCALE3 0.000000 0.000000 0.011000 0.00000