HEADER OXIDOREDUCTASE/INHIBITOR 21-JAN-16 5HQE
TITLE CRYSTAL STRUCTURE OF HUMAN DIHYDROOROTATE DEHYDROGENASE (DHODH) WITH
TITLE 2 COMPOUND 18T
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 29-395;
COMPND 5 SYNONYM: DHODEHASE,DIHYDROOROTATE OXIDASE;
COMPND 6 EC: 1.3.5.2;
COMPND 7 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: DHODH;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21
KEYWDS ENZYME, OXIDOREDUCTASE-INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR J.HUANG,D.WU,Q.LU
REVDAT 2 20-MAR-24 5HQE 1 JRNL REMARK
REVDAT 1 27-JUL-16 5HQE 0
JRNL AUTH J.HUANG,D.WU,Q.LU
JRNL TITL CRYSTAL STRUCTURE OF HUMAN DIHYDROOROTATE DEHYDROGENASE
JRNL TITL 2 (DHODH) WITH 18T AT 1.62 A RESOLUTION
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.62 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.7.0032
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) : 1.62
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.24
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 70538
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) : 0.161
REMARK 3 R VALUE (WORKING SET) : 0.160
REMARK 3 FREE R VALUE : 0.182
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 3743
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) : 1.62
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66
REMARK 3 REFLECTION IN BIN (WORKING SET) : 5123
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.89
REMARK 3 BIN R VALUE (WORKING SET) : 0.1790
REMARK 3 BIN FREE R VALUE SET COUNT : 252
REMARK 3 BIN FREE R VALUE : 0.2140
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2790
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 91
REMARK 3 SOLVENT ATOMS : 162
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.41
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) : -0.01000
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): 0.060
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.062
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.033
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.911
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2924 ; 0.028 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 2855 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3958 ; 2.704 ; 2.017
REMARK 3 BOND ANGLES OTHERS (DEGREES): 6539 ; 1.054 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 364 ; 5.926 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;34.850 ;22.880
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 493 ;13.334 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;20.994 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 440 ; 0.153 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3306 ; 0.015 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 649 ; 0.001 ; 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): 1462 ; 2.187 ; 1.819
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1458 ; 2.115 ; 1.809
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1822 ; 3.002 ; 2.712
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1823 ; 3.004 ; 2.716
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1461 ; 3.850 ; 2.297
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1462 ; 3.849 ; 2.297
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2137 ; 5.684 ; 3.280
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3336 ; 6.516 ;15.361
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3337 ; 6.524 ;15.367
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
REMARK 4
REMARK 4 5HQE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JAN-16.
REMARK 100 THE DEPOSITION ID IS D_1000217088.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 05-APR-15
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 4.8-5.4
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRF
REMARK 200 BEAMLINE : BL19U1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.987
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PHENIX
REMARK 200 DATA SCALING SOFTWARE : HKL-3000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70538
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620
REMARK 200 RESOLUTION RANGE LOW (A) : 39.240
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 20.00
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
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: COOT
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 64.04
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.42
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M ACETATE, 40MM C11DAO, 20.8MM N,N
REMARK 280 -DIMETHYLDECYLAMINE-N-OXIDE (DDAO), 2MM DHO, 1.6-1.8 M AMMONIUM
REMARK 280 SULFATE, PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+1/3
REMARK 290 6555 -X,-X+Y,-Z+2/3
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 82.01333
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.00667
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.00667
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 82.01333
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 240 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 14960 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET A 7
REMARK 465 GLY A 8
REMARK 465 HIS A 9
REMARK 465 HIS A 10
REMARK 465 HIS A 11
REMARK 465 HIS A 12
REMARK 465 HIS A 13
REMARK 465 HIS A 14
REMARK 465 HIS A 15
REMARK 465 HIS A 16
REMARK 465 HIS A 17
REMARK 465 HIS A 18
REMARK 465 SER A 19
REMARK 465 SER A 20
REMARK 465 GLY A 21
REMARK 465 HIS A 22
REMARK 465 ILE A 23
REMARK 465 ASP A 24
REMARK 465 ASP A 25
REMARK 465 ASP A 26
REMARK 465 ASP A 27
REMARK 465 LYS A 28
REMARK 465 HIS A 29
REMARK 465 MET A 30
REMARK 465 ALA A 31
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 LYS A 124 CE NZ
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 195 CE1 TYR A 195 CZ -0.089
REMARK 500 GLU A 266 CD GLU A 266 OE2 -0.076
REMARK 500 GLU A 319 CD GLU A 319 OE1 0.073
REMARK 500 GLU A 344 CD GLU A 344 OE2 0.076
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 61 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 ARG A 133 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES
REMARK 500 ARG A 136 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 ARG A 136 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES
REMARK 500 ASP A 207 CB - CG - OD1 ANGL. DEV. = -6.2 DEGREES
REMARK 500 ASP A 207 CB - CG - OD2 ANGL. DEV. = 8.0 DEGREES
REMARK 500 ARG A 249 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 ARG A 298 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES
REMARK 500 ASP A 311 CB - CG - OD1 ANGL. DEV. = 9.6 DEGREES
REMARK 500 ARG A 347 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES
REMARK 500 ASP A 393 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES
REMARK 500 ASP A 393 CB - CG - OD2 ANGL. DEV. = -6.0 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 HIS A 41 -60.02 -120.09
REMARK 500 ALA A 71 72.01 -101.46
REMARK 500 ARG A 133 14.62 -143.30
REMARK 500 TYR A 356 -62.02 -138.02
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 64B A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue FMN A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ORO A 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 405
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 406
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 407
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 408
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 409
DBREF 5HQE A 30 396 UNP Q02127 PYRD_HUMAN 29 395
SEQADV 5HQE MET A 7 UNP Q02127 INITIATING METHIONINE
SEQADV 5HQE GLY A 8 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE HIS A 9 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE HIS A 10 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE HIS A 11 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE HIS A 12 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE HIS A 13 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE HIS A 14 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE HIS A 15 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE HIS A 16 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE HIS A 17 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE HIS A 18 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE SER A 19 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE SER A 20 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE GLY A 21 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE HIS A 22 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE ILE A 23 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE ASP A 24 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE ASP A 25 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE ASP A 26 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE ASP A 27 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE LYS A 28 UNP Q02127 EXPRESSION TAG
SEQADV 5HQE HIS A 29 UNP Q02127 EXPRESSION TAG
SEQRES 1 A 390 MET GLY HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS SER
SEQRES 2 A 390 SER GLY HIS ILE ASP ASP ASP ASP LYS HIS MET ALA THR
SEQRES 3 A 390 GLY ASP GLU ARG PHE TYR ALA GLU HIS LEU MET PRO THR
SEQRES 4 A 390 LEU GLN GLY LEU LEU ASP PRO GLU SER ALA HIS ARG LEU
SEQRES 5 A 390 ALA VAL ARG PHE THR SER LEU GLY LEU LEU PRO ARG ALA
SEQRES 6 A 390 ARG PHE GLN ASP SER ASP MET LEU GLU VAL ARG VAL LEU
SEQRES 7 A 390 GLY HIS LYS PHE ARG ASN PRO VAL GLY ILE ALA ALA GLY
SEQRES 8 A 390 PHE ASP LYS HIS GLY GLU ALA VAL ASP GLY LEU TYR LYS
SEQRES 9 A 390 MET GLY PHE GLY PHE VAL GLU ILE GLY SER VAL THR PRO
SEQRES 10 A 390 LYS PRO GLN GLU GLY ASN PRO ARG PRO ARG VAL PHE ARG
SEQRES 11 A 390 LEU PRO GLU ASP GLN ALA VAL ILE ASN ARG TYR GLY PHE
SEQRES 12 A 390 ASN SER HIS GLY LEU SER VAL VAL GLU HIS ARG LEU ARG
SEQRES 13 A 390 ALA ARG GLN GLN LYS GLN ALA LYS LEU THR GLU ASP GLY
SEQRES 14 A 390 LEU PRO LEU GLY VAL ASN LEU GLY LYS ASN LYS THR SER
SEQRES 15 A 390 VAL ASP ALA ALA GLU ASP TYR ALA GLU GLY VAL ARG VAL
SEQRES 16 A 390 LEU GLY PRO LEU ALA ASP TYR LEU VAL VAL ASN VAL SER
SEQRES 17 A 390 SER PRO ASN THR ALA GLY LEU ARG SER LEU GLN GLY LYS
SEQRES 18 A 390 ALA GLU LEU ARG ARG LEU LEU THR LYS VAL LEU GLN GLU
SEQRES 19 A 390 ARG ASP GLY LEU ARG ARG VAL HIS ARG PRO ALA VAL LEU
SEQRES 20 A 390 VAL LYS ILE ALA PRO ASP LEU THR SER GLN ASP LYS GLU
SEQRES 21 A 390 ASP ILE ALA SER VAL VAL LYS GLU LEU GLY ILE ASP GLY
SEQRES 22 A 390 LEU ILE VAL THR ASN THR THR VAL SER ARG PRO ALA GLY
SEQRES 23 A 390 LEU GLN GLY ALA LEU ARG SER GLU THR GLY GLY LEU SER
SEQRES 24 A 390 GLY LYS PRO LEU ARG ASP LEU SER THR GLN THR ILE ARG
SEQRES 25 A 390 GLU MET TYR ALA LEU THR GLN GLY ARG VAL PRO ILE ILE
SEQRES 26 A 390 GLY VAL GLY GLY VAL SER SER GLY GLN ASP ALA LEU GLU
SEQRES 27 A 390 LYS ILE ARG ALA GLY ALA SER LEU VAL GLN LEU TYR THR
SEQRES 28 A 390 ALA LEU THR PHE TRP GLY PRO PRO VAL VAL GLY LYS VAL
SEQRES 29 A 390 LYS ARG GLU LEU GLU ALA LEU LEU LYS GLU GLN GLY PHE
SEQRES 30 A 390 GLY GLY VAL THR ASP ALA ILE GLY ALA ASP HIS ARG ARG
HET 64B A 401 22
HET FMN A 402 31
HET ORO A 403 11
HET SO4 A 404 5
HET SO4 A 405 5
HET SO4 A 406 5
HET ACT A 407 4
HET ACT A 408 4
HET ACT A 409 4
HETNAM 64B METHYL (2Z)-CYANO[3-(2-FLUORO-4-METHOXYPHENYL)-4-OXO-1,
HETNAM 2 64B 3-THIAZOLIDIN-2-YLIDENE]ACETATE
HETNAM FMN FLAVIN MONONUCLEOTIDE
HETNAM ORO OROTIC ACID
HETNAM SO4 SULFATE ION
HETNAM ACT ACETATE ION
HETSYN FMN RIBOFLAVIN MONOPHOSPHATE
FORMUL 2 64B C14 H11 F N2 O4 S
FORMUL 3 FMN C17 H21 N4 O9 P
FORMUL 4 ORO C5 H4 N2 O4
FORMUL 5 SO4 3(O4 S 2-)
FORMUL 8 ACT 3(C2 H3 O2 1-)
FORMUL 11 HOH *162(H2 O)
HELIX 1 AA1 THR A 32 HIS A 41 1 10
HELIX 2 AA2 HIS A 41 LEU A 50 1 10
HELIX 3 AA3 ASP A 51 LEU A 65 1 15
HELIX 4 AA4 SER A 76 GLU A 80 5 5
HELIX 5 AA5 ALA A 104 GLY A 112 1 9
HELIX 6 AA6 PRO A 138 ASP A 140 5 3
HELIX 7 AA7 GLY A 153 ALA A 163 1 11
HELIX 8 AA8 ARG A 164 ASP A 174 1 11
HELIX 9 AA9 ASP A 190 GLY A 203 1 14
HELIX 10 AB1 PRO A 204 ALA A 206 5 3
HELIX 11 AB2 GLY A 220 GLN A 225 5 6
HELIX 12 AB3 GLY A 226 GLY A 243 1 18
HELIX 13 AB4 ARG A 245 ARG A 249 5 5
HELIX 14 AB5 THR A 261 GLY A 276 1 16
HELIX 15 AB6 LEU A 309 THR A 324 1 16
HELIX 16 AB7 SER A 338 GLY A 349 1 12
HELIX 17 AB8 TYR A 356 GLY A 363 1 8
HELIX 18 AB9 PRO A 365 GLN A 381 1 17
HELIX 19 AC1 GLY A 385 ILE A 390 1 6
HELIX 20 AC2 GLY A 391 ARG A 395 5 5
SHEET 1 AA1 2 VAL A 81 VAL A 83 0
SHEET 2 AA1 2 HIS A 86 PHE A 88 -1 O PHE A 88 N VAL A 81
SHEET 1 AA2 9 VAL A 92 ILE A 94 0
SHEET 2 AA2 9 PHE A 115 VAL A 121 1 O PHE A 115 N ILE A 94
SHEET 3 AA2 9 LEU A 178 LEU A 182 1 O GLY A 179 N VAL A 116
SHEET 4 AA2 9 TYR A 208 ASN A 212 1 O VAL A 210 N LEU A 182
SHEET 5 AA2 9 ALA A 251 ILE A 256 1 O LEU A 253 N LEU A 209
SHEET 6 AA2 9 GLY A 279 VAL A 282 1 O ILE A 281 N VAL A 254
SHEET 7 AA2 9 ILE A 330 VAL A 333 1 O ILE A 331 N LEU A 280
SHEET 8 AA2 9 LEU A 352 LEU A 355 1 O LEU A 352 N GLY A 332
SHEET 9 AA2 9 VAL A 92 ILE A 94 1 N GLY A 93 O VAL A 353
SHEET 1 AA3 3 VAL A 134 LEU A 137 0
SHEET 2 AA3 3 ALA A 142 ASN A 145 -1 O ALA A 142 N LEU A 137
SHEET 3 AA3 3 GLY A 303 GLY A 306 -1 O GLY A 303 N ASN A 145
CISPEP 1 GLY A 119 SER A 120 0 3.32
CISPEP 2 ARG A 131 PRO A 132 0 1.26
CISPEP 3 VAL A 282 THR A 283 0 13.20
SITE 1 AC1 13 TYR A 38 LEU A 42 MET A 43 LEU A 46
SITE 2 AC1 13 LEU A 58 ALA A 59 PHE A 62 THR A 63
SITE 3 AC1 13 LEU A 67 LEU A 68 PRO A 69 PRO A 364
SITE 4 AC1 13 HOH A 589
SITE 1 AC2 25 ALA A 95 ALA A 96 GLY A 97 LYS A 100
SITE 2 AC2 25 SER A 120 ASN A 145 TYR A 147 ASN A 181
SITE 3 AC2 25 ASN A 212 LYS A 255 THR A 283 ASN A 284
SITE 4 AC2 25 THR A 285 SER A 305 GLY A 306 LEU A 309
SITE 5 AC2 25 VAL A 333 GLY A 334 GLY A 335 LEU A 355
SITE 6 AC2 25 TYR A 356 THR A 357 ORO A 403 HOH A 514
SITE 7 AC2 25 HOH A 533
SITE 1 AC3 11 LYS A 100 ASN A 145 TYR A 147 GLY A 148
SITE 2 AC3 11 PHE A 149 ASN A 212 SER A 215 ASN A 217
SITE 3 AC3 11 ASN A 284 THR A 285 FMN A 402
SITE 1 AC4 4 ALA A 219 GLY A 220 ARG A 222 HOH A 605
SITE 1 AC5 4 ARG A 245 VAL A 247 HIS A 248 HOH A 503
SITE 1 AC6 7 ARG A 57 HIS A 101 ASN A 150 HIS A 152
SITE 2 AC6 7 ACT A 407 HOH A 523 HOH A 567
SITE 1 AC7 4 GLN A 126 GLU A 127 SER A 151 SO4 A 406
SITE 1 AC8 1 GLU A 197
SITE 1 AC9 3 LYS A 170 THR A 261 GLN A 263
CRYST1 90.624 90.624 123.020 90.00 90.00 120.00 P 32 2 1 6
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 0.011035 0.006371 0.000000 0.00000
SCALE2 0.000000 0.012742 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008129 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
