HEADER OXIDOREDUCTASE 25-OCT-17 6ET4 TITLE HUMAN DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH NOVEL INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINALLY TRUNCATED HUMAN DHODH, 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 CELL: U937; SOURCE 6 GENE: DHODH; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET-19B KEYWDS OXIDOREDUCTASE, DHODH, CANCER, P53 ACTIVATION, PYRIMIDINE SYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR M.HAKANSSON,B.WALSE,A.-L.GUSTAVSSON,S.LAIN REVDAT 2 17-JAN-24 6ET4 1 REMARK REVDAT 1 28-MAR-18 6ET4 0 JRNL AUTH M.J.G.W.LADDS,I.M.M.VAN LEEUWEN,C.J.DRUMMOND,S.CHU, JRNL AUTH 2 A.R.HEALY,G.POPOVA,A.PASTOR FERNANDEZ,T.MOLLICK,S.DAREKAR, JRNL AUTH 3 S.K.SEDIMBI,M.NEKULOVA,M.C.C.SACHWEH,J.CAMPBELL,M.HIGGINS, JRNL AUTH 4 C.TUCK,M.POPA,M.M.SAFONT,P.GELEBART,Z.FANDALYUK, JRNL AUTH 5 A.M.THOMPSON,R.SVENSSON,A.L.GUSTAVSSON,L.JOHANSSON, JRNL AUTH 6 K.FARNEGARDH,U.YNGVE,A.SALEH,M.HARALDSSON,A.C.A.D'HOLLANDER, JRNL AUTH 7 M.FRANCO,Y.ZHAO,M.HAKANSSON,B.WALSE,K.LARSSON,E.M.PEAT, JRNL AUTH 8 V.PELECHANO,J.LUNEC,B.VOJTESEK,M.CARMENA,W.C.EARNSHAW, JRNL AUTH 9 A.R.MCCARTHY,N.J.WESTWOOD,M.ARSENIAN-HENRIKSSON,D.P.LANE, JRNL AUTH10 R.BHATIA,E.MCCORMACK,S.LAIN JRNL TITL A DHODH INHIBITOR INCREASES P53 SYNTHESIS AND ENHANCES TUMOR JRNL TITL 2 CELL KILLING BY P53 DEGRADATION BLOCKAGE. JRNL REF NAT COMMUN V. 9 1107 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29549331 JRNL DOI 10.1038/S41467-018-03441-3 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 61296 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) : 0.107 REMARK 3 R VALUE (WORKING SET) : 0.105 REMARK 3 FREE R VALUE : 0.138 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3227 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4104 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.38 REMARK 3 BIN R VALUE (WORKING SET) : 0.1420 REMARK 3 BIN FREE R VALUE SET COUNT : 221 REMARK 3 BIN FREE R VALUE : 0.1900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2804 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 131 REMARK 3 SOLVENT ATOMS : 257 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : -0.07000 REMARK 3 B12 (A**2) : 0.02000 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): 0.059 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.056 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.863 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3117 ; 0.021 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3089 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4233 ; 2.284 ; 2.024 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7103 ; 1.010 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 399 ; 6.284 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;35.037 ;22.932 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 534 ;12.858 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;17.797 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 475 ; 0.136 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3525 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 695 ; 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): 1529 ; 5.435 ; 2.127 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1522 ; 5.397 ; 2.115 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1915 ; 6.086 ; 3.177 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1915 ; 6.086 ; 3.181 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1587 ; 7.969 ; 2.832 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1588 ; 7.966 ; 2.832 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2308 ; 8.602 ; 3.981 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3564 ; 7.217 ;18.339 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3565 ; 7.216 ;18.340 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6205 ; 6.134 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 79 ;32.914 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6330 ;18.716 ; 5.000 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 6ET4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1200007209. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64865 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 10.70 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.1 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4OQV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% GLYCEROL, 100 MM SODIUM ACETATE PH REMARK 280 4.8, 2 M AMMONIUMSULPHATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 81.80000 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 40.90000 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 40.90000 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 81.80000 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: 2770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 857 LIES ON A SPECIAL POSITION. 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 OE1 GLN A 315 OXT ACY A 506 2.13 REMARK 500 O ASN A 212 O HOH A 601 2.14 REMARK 500 O HOH A 781 O HOH A 816 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 195 CE1 TYR A 195 CZ -0.085 REMARK 500 GLY A 226 N GLY A 226 CA 0.094 REMARK 500 GLU A 266 CD GLU A 266 OE1 0.068 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 ASP A 34 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 LYS A 87 CG - CD - CE ANGL. DEV. = 24.8 DEGREES REMARK 500 LYS A 87 CD - CE - NZ ANGL. DEV. = 17.1 DEGREES REMARK 500 ARG A 136 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 160 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 VAL A 213 N - CA - C ANGL. DEV. = -26.6 DEGREES REMARK 500 GLN A 225 CB - CA - C ANGL. DEV. = -12.2 DEGREES REMARK 500 ARG A 249 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 249 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 347 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 372 NE - CZ - NH2 ANGL. DEV. = -3.2 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 -61.16 -126.80 REMARK 500 LEU A 224 26.37 -57.64 REMARK 500 TYR A 356 -66.88 -143.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 226 LYS A 227 -142.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 857 DISTANCE = 6.86 ANGSTROMS REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DOR A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SDV A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DDQ A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACY A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACY A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACY A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACY A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 514 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 515 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 516 REMARK 999 REMARK 999 SEQUENCE REMARK 999 START AT POSITION 31 IN SEQUENCE TGDER.. ETC (FIRST TWO AA REMARK 999 MA HAS BEEN ADDED) DBREF 6ET4 A 30 396 UNP Q02127 PYRD_HUMAN 29 395 SEQRES 1 A 367 MET ALA THR GLY ASP GLU ARG PHE TYR ALA GLU HIS LEU SEQRES 2 A 367 MET PRO THR LEU GLN GLY LEU LEU ASP PRO GLU SER ALA SEQRES 3 A 367 HIS ARG LEU ALA VAL ARG PHE THR SER LEU GLY LEU LEU SEQRES 4 A 367 PRO ARG ALA ARG PHE GLN ASP SER ASP MET LEU GLU VAL SEQRES 5 A 367 ARG VAL LEU GLY HIS LYS PHE ARG ASN PRO VAL GLY ILE SEQRES 6 A 367 ALA ALA GLY PHE ASP LYS HIS GLY GLU ALA VAL ASP GLY SEQRES 7 A 367 LEU TYR LYS MET GLY PHE GLY PHE VAL GLU ILE GLY SER SEQRES 8 A 367 VAL THR PRO LYS PRO GLN GLU GLY ASN PRO ARG PRO ARG SEQRES 9 A 367 VAL PHE ARG LEU PRO GLU ASP GLN ALA VAL ILE ASN ARG SEQRES 10 A 367 TYR GLY PHE ASN SER HIS GLY LEU SER VAL VAL GLU HIS SEQRES 11 A 367 ARG LEU ARG ALA ARG GLN GLN LYS GLN ALA LYS LEU THR SEQRES 12 A 367 GLU ASP GLY LEU PRO LEU GLY VAL ASN LEU GLY LYS ASN SEQRES 13 A 367 LYS THR SER VAL ASP ALA ALA GLU ASP TYR ALA GLU GLY SEQRES 14 A 367 VAL ARG VAL LEU GLY PRO LEU ALA ASP TYR LEU VAL VAL SEQRES 15 A 367 ASN VAL SER SER PRO ASN THR ALA GLY LEU ARG SER LEU SEQRES 16 A 367 GLN GLY LYS ALA GLU LEU ARG ARG LEU LEU THR LYS VAL SEQRES 17 A 367 LEU GLN GLU ARG ASP GLY LEU ARG ARG VAL HIS ARG PRO SEQRES 18 A 367 ALA VAL LEU VAL LYS ILE ALA PRO ASP LEU THR SER GLN SEQRES 19 A 367 ASP LYS GLU ASP ILE ALA SER VAL VAL LYS GLU LEU GLY SEQRES 20 A 367 ILE ASP GLY LEU ILE VAL THR ASN THR THR VAL SER ARG SEQRES 21 A 367 PRO ALA GLY LEU GLN GLY ALA LEU ARG SER GLU THR GLY SEQRES 22 A 367 GLY LEU SER GLY LYS PRO LEU ARG ASP LEU SER THR GLN SEQRES 23 A 367 THR ILE ARG GLU MET TYR ALA LEU THR GLN GLY ARG VAL SEQRES 24 A 367 PRO ILE ILE GLY VAL GLY GLY VAL SER SER GLY GLN ASP SEQRES 25 A 367 ALA LEU GLU LYS ILE ARG ALA GLY ALA SER LEU VAL GLN SEQRES 26 A 367 LEU TYR THR ALA LEU THR PHE TRP GLY PRO PRO VAL VAL SEQRES 27 A 367 GLY LYS VAL LYS ARG GLU LEU GLU ALA LEU LEU LYS GLU SEQRES 28 A 367 GLN GLY PHE GLY GLY VAL THR ASP ALA ILE GLY ALA ASP SEQRES 29 A 367 HIS ARG ARG HET FMN A 501 31 HET DOR A 502 11 HET SDV A 503 28 HET DDQ A 504 14 HET ACY A 505 4 HET ACY A 506 4 HET ACY A 507 4 HET ACY A 508 4 HET GOL A 509 6 HET GOL A 510 6 HET GOL A 511 6 HET SO4 A 512 5 HET SO4 A 513 5 HET CL A 514 1 HET CL A 515 1 HET CL A 516 1 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM DOR (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID HETNAM SDV N-[(4R)-1-(2-FLUOROPHENYL)-4,5,6,7-TETRAHYDROINDAZOL-4- HETNAM 2 SDV YL]-2,1-BENZOXAZOLE-3-CARBOXAMIDE HETNAM DDQ DECYLAMINE-N,N-DIMETHYL-N-OXIDE HETNAM ACY ACETIC ACID HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETSYN FMN RIBOFLAVIN MONOPHOSPHATE HETSYN DOR DIHYDROOROTIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 3 DOR C5 H6 N2 O4 FORMUL 4 SDV C21 H17 F N4 O2 FORMUL 5 DDQ C12 H27 N O FORMUL 6 ACY 4(C2 H4 O2) FORMUL 10 GOL 3(C3 H8 O3) FORMUL 13 SO4 2(O4 S 2-) FORMUL 15 CL 3(CL 1-) FORMUL 18 HOH *257(H2 O) HELIX 1 AA1 ALA A 31 HIS A 41 1 11 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 LEU A 224 5 5 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 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 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 ILE A 144 N PHE A 135 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 4.39 CISPEP 2 ARG A 131 PRO A 132 0 -1.55 CISPEP 3 VAL A 282 THR A 283 0 15.15 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 DOR A 502 HOH A 643 SITE 7 AC1 25 HOH A 651 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 501 SITE 1 AC3 15 TYR A 38 MET A 43 ALA A 55 HIS A 56 SITE 2 AC3 15 ALA A 59 THR A 63 LEU A 67 LEU A 68 SITE 3 AC3 15 VAL A 134 TYR A 356 LEU A 359 THR A 360 SITE 4 AC3 15 PRO A 364 HOH A 700 HOH A 707 SITE 1 AC4 3 TYR A 38 PHE A 62 LEU A 68 SITE 1 AC5 8 GLN A 168 ALA A 169 THR A 172 LEU A 205 SITE 2 AC5 8 ALA A 206 ASP A 207 HOH A 614 HOH A 695 SITE 1 AC6 7 LYS A 307 PRO A 308 ASP A 311 THR A 314 SITE 2 AC6 7 GLN A 315 ARG A 318 HOH A 652 SITE 1 AC7 4 ARG A 57 HIS A 152 HOH A 604 HOH A 608 SITE 1 AC8 8 GLU A 53 ARG A 57 LYS A 100 HIS A 101 SITE 2 AC8 8 TYR A 147 ASN A 150 HOH A 608 HOH A 744 SITE 1 AC9 4 PRO A 123 SER A 155 HOH A 626 HOH A 761 SITE 1 AD1 1 ARG A 160 SITE 1 AD2 3 LYS A 227 ALA A 228 ARG A 231 SITE 1 AD3 4 ARG A 245 VAL A 247 HIS A 248 HOH A 621 SITE 1 AD4 3 ARG A 246 ARG A 249 HOH A 760 SITE 1 AD5 2 ARG A 298 SER A 299 SITE 1 AD6 1 ASP A 34 SITE 1 AD7 1 SER A 262 CRYST1 90.860 90.860 122.700 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 0.011006 0.006354 0.000000 0.00000 SCALE2 0.000000 0.012709 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008150 0.00000