HEADER OXIDOREDUCTASE 28-JAN-09 3G0U TITLE HUMAN DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH A LEFLUNOMIDE TITLE 2 DERIVATIVE INHIBITOR 4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROOROTATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 30-396; COMPND 5 SYNONYM: DHODEHASE, DIHYDROOROTATE OXIDASE; COMPND 6 EC: 1.3.3.1; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-ALPHA-BARREL, TIM-BARREL, FAD, FLAVOPROTEIN, MEMBRANE, KEYWDS 2 MITOCHONDRION, MITOCHONDRION INNER MEMBRANE, OXIDOREDUCTASE, KEYWDS 3 POLYMORPHISM, PYRIMIDINE BIOSYNTHESIS, TRANSIT PEPTIDE EXPDTA X-RAY DIFFRACTION AUTHOR M.DAVIS,T.HEIKKILA,G.A.MCCONKEY,C.W.G.FISHWICK,M.R.PARSONS, AUTHOR 2 A.P.JOHNSON REVDAT 2 01-NOV-23 3G0U 1 REMARK REVDAT 1 09-JUN-09 3G0U 0 JRNL AUTH M.DAVIES,T.HEIKKILA,G.A.MCCONKEY,C.W.G.FISHWICK,M.R.PARSONS, JRNL AUTH 2 A.P.JOHNSON JRNL TITL STRUCTURE-BASED DESIGN, SYNTHESIS, AND CHARACTERIZATION OF JRNL TITL 2 INHIBITORS OF HUMAN AND PLASMODIUM FALCIPARUM DIHYDROOROTATE JRNL TITL 3 DEHYDROGENASES JRNL REF J.MED.CHEM. V. 52 2683 2009 JRNL REFN ISSN 0022-2623 JRNL PMID 19351152 JRNL DOI 10.1021/JM800963T REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 78.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 38077 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2005 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) : 2795 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.1780 REMARK 3 BIN FREE R VALUE SET COUNT : 119 REMARK 3 BIN FREE R VALUE : 0.2250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2758 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 314 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.21000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : -0.32000 REMARK 3 B12 (A**2) : 0.11000 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): 0.121 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.119 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.178 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2884 ; 0.032 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3904 ; 2.253 ; 2.011 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 359 ; 5.952 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 124 ;37.125 ;23.145 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 494 ;14.202 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;20.567 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 436 ; 0.224 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2179 ; 0.015 ; 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): 1786 ; 1.435 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2867 ; 2.339 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1098 ; 4.066 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1037 ; 6.573 ; 4.500 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 : MASK 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 3G0U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000051280. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-06 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 : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40082 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 78.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 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: PHASER REMARK 200 STARTING MODEL: 1D3H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROPS: 20MG/ML PROTEIN IN 50MM HEPES, REMARK 280 PH 7.7, 400MM NACL, 30% GLYCEROL, 1MM EDTA, 10MM N,N- REMARK 280 DIMETHYLUNDECYLAMIN-N-OXIDE (C11DAO) PRECIPITANT SOLUTION: 0.1M REMARK 280 ACETATE PH 4.6-5.0, 40MM C11DAO, 20.8MM N,N-DIMETHYLDECYLAMINE-N- REMARK 280 OXIDE (DDAO), 2MM DIHYDROOROTATE (DHO), 1.8-2.4M AMMONIUM REMARK 280 SULFATE, 1MM INHIBITORS RESERVOIR: 0.1M ACETATE PH 4.8, 2.4-2.6M REMARK 280 AMMONIUM SULFATE, 30% GLYCEROL , VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 81.86600 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 40.93300 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 40.93300 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 81.86600 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 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 30 REMARK 465 ALA A 31 REMARK 465 THR A 32 REMARK 465 ARG A 70 REMARK 465 ALA A 71 REMARK 465 ARG A 72 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 CG1 VAL A 213 O HOH A 659 1.61 REMARK 500 CD GLU A 240 O HOH A 663 1.70 REMARK 500 CG2 VAL A 210 O HOH A 655 1.70 REMARK 500 N HIS A 86 O HOH A 657 1.70 REMARK 500 CB VAL A 210 O HOH A 655 1.78 REMARK 500 O HOH A 603 O HOH A 610 1.78 REMARK 500 NH1 ARG A 136 O HOH A 522 1.80 REMARK 500 O HOH A 4 O HOH A 603 1.82 REMARK 500 O HOH A 4 O HOH A 609 1.86 REMARK 500 CA LEU A 68 O HOH A 667 1.93 REMARK 500 CG ARG A 36 OE2 GLU A 40 1.93 REMARK 500 O HOH A 564 O HOH A 648 2.01 REMARK 500 N GLY A 33 O HOH A 665 2.06 REMARK 500 CA HIS A 86 O HOH A 657 2.07 REMARK 500 O HOH A 608 O HOH A 677 2.08 REMARK 500 O LYS A 273 O HOH A 536 2.11 REMARK 500 N PHE A 73 O HOH A 653 2.12 REMARK 500 C VAL A 180 O HOH A 660 2.13 REMARK 500 O HOH A 413 O HOH A 662 2.17 REMARK 500 O HOH A 603 O HOH A 609 2.17 REMARK 500 O HOH A 429 O HOH A 641 2.17 REMARK 500 O HOH A 441 O HOH A 629 2.17 REMARK 500 CG GLU A 240 O HOH A 663 2.19 REMARK 500 O HOH A 22 O HOH A 600 2.19 REMARK 500 OE2 GLU A 240 O HOH A 663 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CD ARG A 396 O HOH A 638 4555 1.95 REMARK 500 NE2 GLN A 325 O HOH A 654 6664 2.13 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 GLU A 139 CD GLU A 139 OE2 0.067 REMARK 500 GLU A 158 CB GLU A 158 CG 0.114 REMARK 500 ALA A 169 CA ALA A 169 CB 0.150 REMARK 500 VAL A 201 CB VAL A 201 CG2 0.134 REMARK 500 VAL A 252 CB VAL A 252 CG2 0.144 REMARK 500 VAL A 271 CB VAL A 271 CG1 0.129 REMARK 500 VAL A 333 CB VAL A 333 CG2 -0.126 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 VAL A 83 CB - CA - C ANGL. DEV. = -15.9 DEGREES REMARK 500 ARG A 136 NE - CZ - NH1 ANGL. DEV. = -5.1 DEGREES REMARK 500 ARG A 136 NE - CZ - NH2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 162 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 200 NE - CZ - NH1 ANGL. DEV. = -5.3 DEGREES REMARK 500 VAL A 333 CB - CA - C ANGL. DEV. = -14.5 DEGREES REMARK 500 VAL A 333 CG1 - CB - CG2 ANGL. DEV. = 11.1 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 LEU A 67 44.45 -78.36 REMARK 500 LEU A 84 18.03 55.53 REMARK 500 ASP A 99 78.98 -112.26 REMARK 500 ARG A 133 10.90 -141.26 REMARK 500 ARG A 146 55.48 -140.45 REMARK 500 ASN A 284 -171.23 -69.95 REMARK 500 TYR A 356 -63.33 -138.15 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 ORO A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 398 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MDY A 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3F1Q RELATED DB: PDB REMARK 900 RELATED ID: 3FJ6 RELATED DB: PDB REMARK 900 RELATED ID: 3FJL RELATED DB: PDB DBREF 3G0U 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 ORO A 1 11 HET FMN A 398 31 HET MDY A 2 24 HETNAM ORO OROTIC ACID HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM MDY (2Z)-N-(3-CHLORO-2'-METHOXYBIPHENYL-4-YL)-2-CYANO-3- HETNAM 2 MDY HYDROXYBUT-2-ENAMIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 ORO C5 H4 N2 O4 FORMUL 3 FMN C17 H21 N4 O9 P FORMUL 4 MDY C18 H15 CL N2 O3 FORMUL 5 HOH *314(H2 O) HELIX 1 1 ASP A 34 HIS A 41 1 8 HELIX 2 2 HIS A 41 LEU A 50 1 10 HELIX 3 3 ASP A 51 LEU A 65 1 15 HELIX 4 4 SER A 76 GLU A 80 5 5 HELIX 5 5 ALA A 104 GLY A 112 1 9 HELIX 6 6 PRO A 138 ASP A 140 5 3 HELIX 7 7 GLY A 153 ALA A 163 1 11 HELIX 8 8 ARG A 164 ASP A 174 1 11 HELIX 9 9 ASP A 190 GLY A 203 1 14 HELIX 10 10 PRO A 204 ALA A 206 5 3 HELIX 11 11 GLY A 220 GLN A 225 5 6 HELIX 12 12 GLY A 226 GLY A 243 1 18 HELIX 13 13 ARG A 245 ARG A 249 5 5 HELIX 14 14 THR A 261 GLY A 276 1 16 HELIX 15 15 LEU A 309 THR A 324 1 16 HELIX 16 16 SER A 338 GLY A 349 1 12 HELIX 17 17 TYR A 356 GLY A 363 1 8 HELIX 18 18 PRO A 365 GLN A 381 1 17 HELIX 19 19 GLY A 385 ILE A 390 1 6 HELIX 20 20 GLY A 391 ARG A 396 5 6 SHEET 1 A 2 VAL A 81 VAL A 83 0 SHEET 2 A 2 HIS A 86 PHE A 88 -1 O PHE A 88 N VAL A 81 SHEET 1 B 9 VAL A 92 ILE A 94 0 SHEET 2 B 9 PHE A 115 VAL A 121 1 O PHE A 115 N ILE A 94 SHEET 3 B 9 LEU A 178 LEU A 182 1 O GLY A 179 N VAL A 116 SHEET 4 B 9 TYR A 208 ASN A 212 1 O VAL A 210 N LEU A 182 SHEET 5 B 9 ALA A 251 ILE A 256 1 O LEU A 253 N VAL A 211 SHEET 6 B 9 GLY A 279 VAL A 282 1 O ILE A 281 N VAL A 254 SHEET 7 B 9 ILE A 330 VAL A 333 1 O ILE A 331 N VAL A 282 SHEET 8 B 9 LEU A 352 LEU A 355 1 O LEU A 352 N GLY A 332 SHEET 9 B 9 VAL A 92 ILE A 94 1 N GLY A 93 O VAL A 353 SHEET 1 C 3 VAL A 134 LEU A 137 0 SHEET 2 C 3 ALA A 142 ASN A 145 -1 O ALA A 142 N LEU A 137 SHEET 3 C 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 8.33 CISPEP 2 ARG A 131 PRO A 132 0 2.17 CISPEP 3 VAL A 282 THR A 283 0 11.57 SITE 1 AC1 11 LYS A 100 ASN A 145 TYR A 147 GLY A 148 SITE 2 AC1 11 PHE A 149 ASN A 212 SER A 215 ASN A 217 SITE 3 AC1 11 ASN A 284 THR A 285 FMN A 398 SITE 1 AC2 25 ORO A 1 ALA A 95 ALA A 96 GLY A 97 SITE 2 AC2 25 LYS A 100 GLY A 119 SER A 120 ASN A 145 SITE 3 AC2 25 ASN A 181 ASN A 212 LYS A 255 THR A 283 SITE 4 AC2 25 ASN A 284 THR A 285 SER A 305 GLY A 306 SITE 5 AC2 25 LEU A 309 VAL A 333 GLY A 334 GLY A 335 SITE 6 AC2 25 LEU A 355 TYR A 356 THR A 357 HOH A 611 SITE 7 AC2 25 HOH A 615 SITE 1 AC3 13 TYR A 38 MET A 43 PRO A 52 HIS A 56 SITE 2 AC3 13 ALA A 59 THR A 63 PHE A 98 ARG A 136 SITE 3 AC3 13 TYR A 356 LEU A 359 THR A 360 PRO A 364 SITE 4 AC3 13 HOH A 500 CRYST1 90.752 90.752 122.799 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 0.011019 0.006362 0.000000 0.00000 SCALE2 0.000000 0.012724 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008143 0.00000