HEADER OXIDOREDUCTASE 02-MAR-18 5ZFB TITLE STRUCTURE OF HUMAN DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH TITLE 2 ASCOFURANONE (OPEN-FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DHODEHASE,DIHYDROOROTATE OXIDASE; COMPND 5 EC: 1.3.5.2; COMPND 6 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PYRD; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET19B KEYWDS ROSSMANN FOLD, DIHYDROOROTATE/OROTATE, UBIQUINONE/UBIQUINOL, KEYWDS 2 MITOCHONDRIAL INNER MEMBRANE, INHIBITOR COMPLEX, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.MIYAZAKI,K.D.INAOKA,T.SHIBA,H.SAIMOTO,E.AMALIA,Y.KIDO,C.SAKAI, AUTHOR 2 M.NAKAMURA,L.A.MOORE,S.HARADA,K.KITA REVDAT 3 22-NOV-23 5ZFB 1 JRNL REVDAT 2 03-OCT-18 5ZFB 1 JRNL REVDAT 1 26-SEP-18 5ZFB 0 JRNL AUTH Y.MIYAZAKI,D.K.INAOKA,T.SHIBA,H.SAIMOTO,T.SAKURA,E.AMALIA, JRNL AUTH 2 Y.KIDO,C.SAKAI,M.NAKAMURA,A.L.MOORE,S.HARADA,K.KITA JRNL TITL SELECTIVE CYTOTOXICITY OF DIHYDROOROTATE DEHYDROGENASE JRNL TITL 2 INHIBITORS TO HUMAN CANCER CELLS UNDER HYPOXIA AND JRNL TITL 3 NUTRIENT-DEPRIVED CONDITIONS. JRNL REF FRONT PHARMACOL V. 9 997 2018 JRNL REFN ESSN 1663-9812 JRNL PMID 30233375 JRNL DOI 10.3389/FPHAR.2018.00997 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 37505 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1976 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) : 2718 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.1830 REMARK 3 BIN FREE R VALUE SET COUNT : 155 REMARK 3 BIN FREE R VALUE : 0.1990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2805 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 105 REMARK 3 SOLVENT ATOMS : 183 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.119 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.112 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.415 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3027 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4115 ; 1.548 ; 2.016 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 384 ; 5.751 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 129 ;37.094 ;23.101 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 510 ;14.591 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;17.328 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 457 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2304 ; 0.008 ; 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): 1513 ; 1.728 ; 2.176 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1904 ; 2.792 ; 3.236 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1513 ; 2.805 ; 2.687 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): 4775 ; 7.336 ;18.835 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5ZFB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1300006966. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.9 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) : 1.00000 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39966 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3ZWS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM ACETATE, 1.8-1.9M REMARK 280 AMMONIUM SULPHATE, 40MM C11DAO, 20.8MM DDAO, 2MM DIHYDROOROTATE, REMARK 280 PH 4.9, 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 82.47333 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 41.23667 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 41.23667 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 82.47333 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 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 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 LYS A 307 CD - CE - NZ ANGL. DEV. = 20.1 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 -58.90 -123.71 REMARK 500 ASP A 99 77.82 -110.25 REMARK 500 TYR A 356 -62.32 -137.56 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 FMN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ORO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT 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 SO4 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9BX A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 410 DBREF 5ZFB A 30 396 UNP Q02127 PYRD_HUMAN 29 395 SEQADV 5ZFB MET A 7 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB GLY A 8 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB HIS A 9 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB HIS A 10 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB HIS A 11 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB HIS A 12 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB HIS A 13 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB HIS A 14 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB HIS A 15 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB HIS A 16 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB HIS A 17 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB HIS A 18 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB SER A 19 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB SER A 20 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB GLY A 21 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB HIS A 22 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB ILE A 23 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB ASP A 24 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB ASP A 25 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB ASP A 26 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB ASP A 27 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB LYS A 28 UNP Q02127 EXPRESSION TAG SEQADV 5ZFB 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 FMN A 401 31 HET ORO A 402 11 HET ACT A 403 4 HET SO4 A 404 5 HET SO4 A 405 5 HET SO4 A 406 5 HET SO4 A 407 5 HET SO4 A 408 5 HET 9BX A 409 29 HET SO4 A 410 5 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM ORO OROTIC ACID HETNAM ACT ACETATE ION HETNAM SO4 SULFATE ION HETNAM 9BX 3-CHLORO-4,6-DIHYDROXY-5-[(2Z,6Z,8E)-11-HYDROXY-3,7,11- HETNAM 2 9BX TRIMETHYL-10-OXODODECA-2,6,8-TRIEN-1-YL]-2- HETNAM 3 9BX METHYLBENZALDEHYDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 3 ORO C5 H4 N2 O4 FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 SO4 6(O4 S 2-) FORMUL 10 9BX C23 H29 CL O5 FORMUL 12 HOH *183(H2 O) HELIX 1 AA1 ASP A 34 HIS A 41 1 8 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 MET A 111 1 8 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 396 5 6 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 VAL A 211 SHEET 6 AA2 9 GLY A 279 VAL A 282 1 O ILE A 281 N ILE A 256 SHEET 7 AA2 9 ILE A 330 VAL A 333 1 O ILE A 331 N VAL A 282 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 SER A 305 N VAL A 143 CISPEP 1 THR A 32 GLY A 33 0 -2.39 CISPEP 2 GLY A 119 SER A 120 0 6.54 CISPEP 3 ARG A 131 PRO A 132 0 -6.99 CISPEP 4 VAL A 282 THR A 283 0 13.51 SITE 1 AC1 25 ALA A 95 ALA A 96 GLY A 97 LYS A 100 SITE 2 AC1 25 SER A 120 ASN A 145 TYR A 147 ASN A 181 SITE 3 AC1 25 ASN A 212 LYS A 255 THR A 283 ASN A 284 SITE 4 AC1 25 THR A 285 SER A 305 GLY A 306 LEU A 309 SITE 5 AC1 25 VAL A 333 GLY A 334 GLY A 335 LEU A 355 SITE 6 AC1 25 TYR A 356 THR A 357 ORO A 402 HOH A 505 SITE 7 AC1 25 HOH A 555 SITE 1 AC2 11 LYS A 100 ASN A 145 TYR A 147 GLY A 148 SITE 2 AC2 11 PHE A 149 ASN A 212 SER A 215 ASN A 217 SITE 3 AC2 11 ASN A 284 THR A 285 FMN A 401 SITE 1 AC3 5 ALA A 163 LYS A 167 LYS A 227 GLU A 266 SITE 2 AC3 5 ASP A 267 SITE 1 AC4 2 ARG A 245 HIS A 248 SITE 1 AC5 4 LYS A 170 THR A 261 GLN A 263 HOH A 586 SITE 1 AC6 3 THR A 261 SER A 262 HOH A 586 SITE 1 AC7 7 ARG A 57 HIS A 101 ASN A 150 HIS A 152 SITE 2 AC7 7 HOH A 511 HOH A 577 HOH A 596 SITE 1 AC8 3 ARG A 246 ARG A 249 HOH A 629 SITE 1 AC9 15 MET A 43 LEU A 46 GLN A 47 PRO A 52 SITE 2 AC9 15 ALA A 55 HIS A 56 ALA A 59 PHE A 98 SITE 3 AC9 15 ARG A 136 TYR A 356 LEU A 359 THR A 360 SITE 4 AC9 15 GLY A 363 PRO A 364 HOH A 543 SITE 1 AD1 7 LYS A 307 PRO A 308 ASP A 311 THR A 314 SITE 2 AD1 7 GLN A 315 ARG A 318 HOH A 535 CRYST1 90.323 90.323 123.710 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 0.011071 0.006392 0.000000 0.00000 SCALE2 0.000000 0.012784 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008083 0.00000