HEADER TRANSFERASE/TRANSFERASE INHIBITOR 01-DEC-17 5YX1
TITLE CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE IN COMPLEX
TITLE 2 WITH U004
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,Y.URADE,D.TAKAYA,A.TANAKA
REVDAT 2 22-NOV-23 5YX1 1 LINK
REVDAT 1 05-DEC-18 5YX1 0
JRNL AUTH K.INAKA,N.FURUBAYASHI,M.KAMO,K.ARITAKE,Y.URADE,D.TAKAYA,
JRNL AUTH 2 A.TANAKA
JRNL TITL CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE
JRNL TITL 2 IN COMPLEX WITH U004
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.39 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) : 1.39
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.94
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 80.4
REMARK 3 NUMBER OF REFLECTIONS : 123473
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) : 0.186
REMARK 3 R VALUE (WORKING SET) : 0.185
REMARK 3 FREE R VALUE : 0.216
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 6537
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) : 1.39
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.43
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2386
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 20.89
REMARK 3 BIN R VALUE (WORKING SET) : 0.2510
REMARK 3 BIN FREE R VALUE SET COUNT : 117
REMARK 3 BIN FREE R VALUE : 0.2950
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 : 187
REMARK 3 SOLVENT ATOMS : 895
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.62
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.02000
REMARK 3 B22 (A**2) : -0.16000
REMARK 3 B33 (A**2) : 0.16000
REMARK 3 B12 (A**2) : 0.05000
REMARK 3 B13 (A**2) : 0.03000
REMARK 3 B23 (A**2) : 0.04000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.080
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.082
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.133
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6912 ; 0.010 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 6550 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9397 ; 1.566 ; 1.979
REMARK 3 BOND ANGLES OTHERS (DEGREES): 15070 ; 0.801 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 788 ; 5.359 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 332 ;35.210 ;24.217
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1168 ;12.420 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;13.730 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1029 ; 0.083 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7681 ; 0.007 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 1623 ; 0.003 ; 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 5YX1 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_1300006045.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 22-NOV-16
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 : SPRING-8
REMARK 200 BEAMLINE : BL41XU
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 144547
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390
REMARK 200 RESOLUTION RANGE LOW (A) : 70.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 89.3
REMARK 200 DATA REDUNDANCY : 3.100
REMARK 200 R MERGE (I) : 0.09600
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40
REMARK 200 COMPLETENESS FOR SHELL (%) : 86.5
REMARK 200 DATA REDUNDANCY IN SHELL : 2.80
REMARK 200 R MERGE FOR SHELL (I) : 0.57000
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 (%): 44.84
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PEG 6000, 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: 4370 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 18230 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: 4390 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 18190 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 A 301 O HOH A 338 2.14
REMARK 500 NH1 ARG D 193 O HOH D 401 2.18
REMARK 500 NZ LYS A 73 OE1 GLN B 85 2.19
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 B 14 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 ARG B 14 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 GLN A 63 107.15 75.58
REMARK 500 GLN B 63 109.45 76.68
REMARK 500 GLN C 63 109.72 73.24
REMARK 500 LYS C 108 98.05 -62.01
REMARK 500 GLN D 63 109.19 76.15
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 A 201 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 339 O
REMARK 620 2 HOH A 353 O 87.2
REMARK 620 3 HOH A 370 O 91.9 81.3
REMARK 620 4 HOH B 426 O 93.3 165.8 84.5
REMARK 620 5 HOH B 523 O 75.7 88.2 164.2 105.7
REMARK 620 6 HOH B 527 O 172.8 90.1 94.3 91.0 97.5
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 328 O
REMARK 620 2 HOH C 332 O 87.4
REMARK 620 3 HOH C 361 O 87.7 79.3
REMARK 620 4 HOH D 430 O 87.0 82.8 161.5
REMARK 620 5 HOH D 462 O 84.1 170.0 105.5 91.6
REMARK 620 6 HOH D 497 O 176.9 91.5 95.0 89.9 96.7
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 MG A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GSH A 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GSH B 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue UX4 B 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GSH C 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue UX4 C 203
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GSH D 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue UX4 D 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 303
DBREF 5YX1 A 2 199 UNP O60760 HPGDS_HUMAN 2 199
DBREF 5YX1 B 2 199 UNP O60760 HPGDS_HUMAN 2 199
DBREF 5YX1 C 2 199 UNP O60760 HPGDS_HUMAN 2 199
DBREF 5YX1 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 MG A 201 1
HET GSH A 202 20
HET GSH B 301 20
HET UX4 B 302 31
HET GOL B 303 6
HET MG C 201 1
HET GSH C 202 20
HET UX4 C 203 31
HET GSH D 301 20
HET UX4 D 302 31
HET GOL D 303 6
HETNAM MG MAGNESIUM ION
HETNAM GSH GLUTATHIONE
HETNAM UX4 ETHYL 4-[(8R)-3,8-DIMETHYL-4-OXO-4,6,7,8,9,10-
HETNAM 2 UX4 HEXAHYDROTHIENO[2',3':4,5]PYRIMIDO[1,2-A]AZEPIN-2-
HETNAM 3 UX4 YL]CARBAMOYLPIPERAZINE-1-CARBOXYLATE
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 5 MG 2(MG 2+)
FORMUL 6 GSH 4(C10 H17 N3 O6 S)
FORMUL 8 UX4 3(C21 H29 N5 O4 S)
FORMUL 9 GOL 2(C3 H8 O3)
FORMUL 16 HOH *895(H2 O)
HELIX 1 AA1 ALA A 15 LEU A 25 1 11
HELIX 2 AA2 GLU A 35 ALA A 37 5 3
HELIX 3 AA3 ASP A 38 SER A 44 1 7
HELIX 4 AA4 GLN A 63 LYS A 73 1 11
HELIX 5 AA5 THR A 81 PHE A 102 1 22
HELIX 6 AA6 LYS A 108 TYR A 122 1 15
HELIX 7 AA7 ASN A 123 GLY A 136 1 14
HELIX 8 AA8 THR A 147 LYS A 164 1 18
HELIX 9 AA9 HIS A 171 ILE A 184 1 14
HELIX 10 AB1 ILE A 184 ARG A 194 1 11
HELIX 11 AB2 ARG B 12 ARG B 14 5 3
HELIX 12 AB3 ALA B 15 LEU B 25 1 11
HELIX 13 AB4 GLU B 35 ALA B 37 5 3
HELIX 14 AB5 ASP B 38 SER B 44 1 7
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 LYS B 108 ASN B 123 1 16
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 ARG C 12 ARG C 14 5 3
HELIX 23 AC5 ALA C 15 ASP C 26 1 12
HELIX 24 AC6 GLU C 35 ALA C 37 5 3
HELIX 25 AC7 ASP C 38 SER C 44 1 7
HELIX 26 AC8 GLN C 63 LYS C 73 1 11
HELIX 27 AC9 THR C 81 PHE C 102 1 22
HELIX 28 AD1 LYS C 108 TYR C 122 1 15
HELIX 29 AD2 TYR C 122 GLY C 136 1 15
HELIX 30 AD3 THR C 147 LYS C 164 1 18
HELIX 31 AD4 HIS C 171 ILE C 184 1 14
HELIX 32 AD5 ILE C 184 ARG C 194 1 11
HELIX 33 AD6 ARG D 12 ARG D 14 5 3
HELIX 34 AD7 ALA D 15 ASP D 26 1 12
HELIX 35 AD8 GLU D 35 ALA D 37 5 3
HELIX 36 AD9 ASP D 38 SER D 44 1 7
HELIX 37 AE1 GLN D 63 LYS D 73 1 11
HELIX 38 AE2 THR D 81 CYS D 101 1 21
HELIX 39 AE3 LYS D 108 ASN D 123 1 16
HELIX 40 AE4 ASN D 123 GLY D 136 1 14
HELIX 41 AE5 THR D 147 LYS D 164 1 18
HELIX 42 AE6 HIS D 171 ILE D 184 1 14
HELIX 43 AE7 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 TYR A 4 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 59 N VAL A 56
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 8 O ILE B 34
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 TYR C 8 O ILE C 34
SHEET 3 AA3 4 ILE C 53 VAL C 56 -1 O GLU C 55 N LYS C 5
SHEET 4 AA3 4 LEU C 59 HIS C 62 -1 O LEU C 61 N LEU C 54
SHEET 1 AA4 4 GLU D 30 ILE D 34 0
SHEET 2 AA4 4 TYR D 4 PHE D 9 1 N LEU D 6 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 59 N VAL D 56
LINK MG MG A 201 O HOH A 339 1555 1555 2.03
LINK MG MG A 201 O HOH A 353 1555 1555 1.98
LINK MG MG A 201 O HOH A 370 1555 1555 2.09
LINK MG MG A 201 O HOH B 426 1555 1555 2.06
LINK MG MG A 201 O HOH B 523 1555 1555 2.11
LINK MG MG A 201 O HOH B 527 1555 1555 2.16
LINK MG MG C 201 O HOH C 328 1555 1555 2.01
LINK MG MG C 201 O HOH C 332 1555 1555 2.15
LINK MG MG C 201 O HOH C 361 1555 1555 1.93
LINK MG MG C 201 O HOH D 430 1555 1555 2.10
LINK MG MG C 201 O HOH D 462 1555 1555 1.98
LINK MG MG C 201 O HOH D 497 1555 1555 2.11
CISPEP 1 ILE A 51 PRO A 52 0 12.08
CISPEP 2 ILE B 51 PRO B 52 0 9.21
CISPEP 3 ILE C 51 PRO C 52 0 9.66
CISPEP 4 ILE D 51 PRO D 52 0 9.24
SITE 1 AC1 6 HOH A 339 HOH A 353 HOH A 370 HOH B 426
SITE 2 AC1 6 HOH B 523 HOH B 527
SITE 1 AC2 14 TYR A 8 ARG A 14 TRP A 39 LYS A 43
SITE 2 AC2 14 LYS A 50 ILE A 51 PRO A 52 GLN A 63
SITE 3 AC2 14 SER A 64 HOH A 318 HOH A 359 HOH A 372
SITE 4 AC2 14 HOH A 378 ASP B 97
SITE 1 AC3 16 ASP A 97 TYR B 8 ARG B 14 TRP B 39
SITE 2 AC3 16 LYS B 50 ILE B 51 PRO B 52 GLN B 63
SITE 3 AC3 16 SER B 64 UX4 B 302 HOH B 409 HOH B 423
SITE 4 AC3 16 HOH B 439 HOH B 467 HOH B 539 HOH B 552
SITE 1 AC4 10 ASP A 57 MET B 11 GLY B 13 TRP B 39
SITE 2 AC4 10 TRP B 104 TYR B 152 THR B 159 GSH B 301
SITE 3 AC4 10 HOH B 437 HOH B 538
SITE 1 AC5 7 GLN B 196 THR B 197 HOH B 435 HOH B 536
SITE 2 AC5 7 HOH B 564 GLN D 28 TYR D 29
SITE 1 AC6 6 HOH C 328 HOH C 332 HOH C 361 HOH D 430
SITE 2 AC6 6 HOH D 462 HOH D 497
SITE 1 AC7 13 TYR C 8 ARG C 14 TRP C 39 LYS C 43
SITE 2 AC7 13 LYS C 50 ILE C 51 GLN C 63 SER C 64
SITE 3 AC7 13 UX4 C 203 HOH C 317 HOH C 379 HOH C 389
SITE 4 AC7 13 ASP D 97
SITE 1 AC8 8 GLY C 13 ARG C 14 GLN C 36 MET C 99
SITE 2 AC8 8 TRP C 104 THR C 159 GSH C 202 HOH C 320
SITE 1 AC9 16 ASP C 97 TYR D 8 ARG D 14 TRP D 39
SITE 2 AC9 16 LYS D 50 ILE D 51 PRO D 52 GLN D 63
SITE 3 AC9 16 SER D 64 UX4 D 302 HOH D 403 HOH D 459
SITE 4 AC9 16 HOH D 466 HOH D 492 HOH D 542 HOH D 555
SITE 1 AD1 12 ASP C 57 LEU C 59 MET D 11 GLY D 13
SITE 2 AD1 12 GLN D 36 TRP D 39 TRP D 104 TYR D 152
SITE 3 AD1 12 THR D 159 GSH D 301 HOH D 404 HOH D 464
SITE 1 AD2 8 GLN B 28 TYR B 29 GLN D 196 THR D 197
SITE 2 AD2 8 HOH D 452 HOH D 543 HOH D 581 HOH D 597
CRYST1 48.447 47.119 91.924 92.20 98.67 90.00 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 0.020641 0.000001 0.003150 0.00000
SCALE2 0.000000 0.021223 0.000826 0.00000
SCALE3 0.000000 0.000000 0.011013 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
