HEADER OXIDOREDUCTASE 31-MAY-16 5K9D TITLE CRYSTAL STRUCTURE OF HUMAN DIHYDROOROTATE DEHYDROGENASE AT 1.7 A TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS OXIDOREDUCTASE, ALPHA/BETA BARREL EXPDTA X-RAY DIFFRACTION AUTHOR T.A.LEWIS,D.B.SYKES,J.M.LAW,B.MUNOZ,D.T.SCADDEN,J.K.RUSTIGUEL, AUTHOR 2 M.C.NONATO,S.L.SCHREIBER REVDAT 3 27-SEP-23 5K9D 1 REMARK REVDAT 2 04-JAN-17 5K9D 1 JRNL REVDAT 1 12-OCT-16 5K9D 0 JRNL AUTH T.A.LEWIS,D.B.SYKES,J.M.LAW,B.MUNOZ,J.K.RUSTIGUEL, JRNL AUTH 2 M.C.NONATO,D.T.SCADDEN,S.L.SCHREIBER JRNL TITL DEVELOPMENT OF ML390: A HUMAN DHODH INHIBITOR THAT INDUCES JRNL TITL 2 DIFFERENTIATION IN ACUTE MYELOID LEUKEMIA. JRNL REF ACS MED CHEM LETT V. 7 1112 2016 JRNL REFN ISSN 1948-5875 JRNL PMID 27994748 JRNL DOI 10.1021/ACSMEDCHEMLETT.6B00316 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART 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) : 26.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 63348 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.160 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 3122 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 26.5708 - 4.7548 1.00 2935 152 0.1773 0.2034 REMARK 3 2 4.7548 - 3.7775 1.00 2812 154 0.1264 0.1510 REMARK 3 3 3.7775 - 3.3010 1.00 2818 113 0.1266 0.1489 REMARK 3 4 3.3010 - 2.9997 1.00 2769 165 0.1274 0.1548 REMARK 3 5 2.9997 - 2.7849 1.00 2770 142 0.1223 0.1363 REMARK 3 6 2.7849 - 2.6209 1.00 2751 132 0.1209 0.1481 REMARK 3 7 2.6209 - 2.4897 1.00 2763 143 0.1151 0.1295 REMARK 3 8 2.4897 - 2.3814 1.00 2741 153 0.1142 0.1516 REMARK 3 9 2.3814 - 2.2898 1.00 2752 134 0.1113 0.1412 REMARK 3 10 2.2898 - 2.2108 1.00 2741 128 0.1254 0.1375 REMARK 3 11 2.2108 - 2.1417 1.00 2714 125 0.1150 0.1492 REMARK 3 12 2.1417 - 2.0805 1.00 2743 159 0.1210 0.1365 REMARK 3 13 2.0805 - 2.0258 1.00 2744 138 0.1402 0.1594 REMARK 3 14 2.0258 - 1.9764 1.00 2746 118 0.1280 0.1443 REMARK 3 15 1.9764 - 1.9314 1.00 2743 131 0.1366 0.1397 REMARK 3 16 1.9314 - 1.8903 1.00 2698 151 0.1650 0.2087 REMARK 3 17 1.8903 - 1.8525 1.00 2710 124 0.1471 0.1542 REMARK 3 18 1.8525 - 1.8176 1.00 2722 150 0.1497 0.1691 REMARK 3 19 1.8176 - 1.7851 1.00 2680 185 0.1670 0.1799 REMARK 3 20 1.7851 - 1.7549 1.00 2658 174 0.1788 0.2398 REMARK 3 21 1.7549 - 1.7266 0.99 2683 130 0.2007 0.2266 REMARK 3 22 1.7266 - 1.7000 0.94 2533 121 0.2241 0.2352 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 2940 REMARK 3 ANGLE : 1.079 3998 REMARK 3 CHIRALITY : 0.070 450 REMARK 3 PLANARITY : 0.008 524 REMARK 3 DIHEDRAL : 13.166 1115 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 38 THROUGH 94 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.5374 126.5194 249.6849 REMARK 3 T TENSOR REMARK 3 T11: 0.0594 T22: 0.0827 REMARK 3 T33: 0.0699 T12: -0.0151 REMARK 3 T13: -0.0065 T23: 0.0051 REMARK 3 L TENSOR REMARK 3 L11: 0.1029 L22: 0.0187 REMARK 3 L33: 0.2071 L12: -0.0323 REMARK 3 L13: 0.0805 L23: -0.0543 REMARK 3 S TENSOR REMARK 3 S11: -0.0637 S12: 0.0681 S13: 0.0464 REMARK 3 S21: 0.0003 S22: -0.0201 S23: -0.0159 REMARK 3 S31: -0.0421 S32: 0.0439 S33: -0.0353 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 95 THROUGH 396 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.9985 117.8618 256.5116 REMARK 3 T TENSOR REMARK 3 T11: 0.0204 T22: 0.0589 REMARK 3 T33: 0.0390 T12: 0.0103 REMARK 3 T13: -0.0094 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.0834 L22: 0.0981 REMARK 3 L33: 0.0670 L12: -0.0540 REMARK 3 L13: 0.0664 L23: -0.0235 REMARK 3 S TENSOR REMARK 3 S11: 0.0089 S12: -0.0210 S13: -0.0115 REMARK 3 S21: -0.0049 S22: -0.0100 S23: -0.0077 REMARK 3 S31: 0.0003 S32: -0.0012 S33: 0.0339 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5K9D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000221835. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-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 : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.45867 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR AND TOROIDAL REMARK 200 BENDABLE MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 7.2.1 REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63435 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 28.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 14.30 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : 0.10800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.3000 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) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.41300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.6.0 REMARK 200 STARTING MODEL: 1D3G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.8 REMARK 280 1.8 M AMMONIUM SULFATE 30% (V/V) GLYCEROL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K 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 81.43467 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 40.71733 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 40.71733 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 81.43467 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 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 895 LIES ON A SPECIAL POSITION. 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 SER A 29 REMARK 465 MET A 30 REMARK 465 ALA A 31 REMARK 465 THR A 32 REMARK 465 GLY A 33 REMARK 465 ASP A 34 REMARK 465 GLU A 35 REMARK 465 ARG A 36 REMARK 465 PHE A 37 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 GLU A 40 CG CD OE1 OE2 REMARK 470 HIS A 41 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 42 CG CD1 CD2 REMARK 470 THR A 45 OG1 CG2 REMARK 470 LEU A 46 CG CD1 CD2 REMARK 470 GLN A 47 CG CD OE1 NE2 REMARK 470 LEU A 49 CG CD1 CD2 REMARK 470 LEU A 68 CG CD1 CD2 REMARK 470 ARG A 70 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 72 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 74 CG CD OE1 NE2 REMARK 470 LYS A 124 CE NZ REMARK 470 GLU A 173 CD OE1 OE2 REMARK 470 GLU A 229 CG CD OE1 OE2 REMARK 470 ARG A 327 CZ NH1 NH2 REMARK 470 ARG A 396 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 735 O HOH A 796 1.84 REMARK 500 O HOH A 808 O HOH A 847 1.88 REMARK 500 O HOH A 526 O HOH A 614 2.02 REMARK 500 O HOH A 740 O HOH A 855 2.03 REMARK 500 O HOH A 653 O HOH A 786 2.04 REMARK 500 O HOH A 725 O HOH A 778 2.08 REMARK 500 O HOH A 778 O HOH A 861 2.09 REMARK 500 O HOH A 741 O HOH A 770 2.10 REMARK 500 O HOH A 689 O HOH A 864 2.12 REMARK 500 O HOH A 759 O HOH A 798 2.12 REMARK 500 OE1 GLU A 319 O HOH A 501 2.15 REMARK 500 OE1 GLU A 319 O HOH A 502 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 O HOH A 631 O HOH A 814 5689 1.86 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 42 -63.52 -105.39 REMARK 500 ASP A 99 79.83 -115.76 REMARK 500 ASP A 190 87.01 -161.59 REMARK 500 TYR A 356 -59.51 -139.38 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 895 DISTANCE = 6.72 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 CE9 A 402 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FNR A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ORO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CE9 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 411 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5K9C RELATED DB: PDB REMARK 900 5K9C CONTAINS THE SAME PROTEIN COMPLEXED WITH INHIBITOR DBREF 5K9D A 30 396 UNP Q02127 PYRD_HUMAN 29 395 SEQADV 5K9D SER A 29 UNP Q02127 EXPRESSION TAG SEQRES 1 A 368 SER MET ALA THR GLY ASP GLU ARG PHE TYR ALA GLU HIS SEQRES 2 A 368 LEU MET PRO THR LEU GLN GLY LEU LEU ASP PRO GLU SER SEQRES 3 A 368 ALA HIS ARG LEU ALA VAL ARG PHE THR SER LEU GLY LEU SEQRES 4 A 368 LEU PRO ARG ALA ARG PHE GLN ASP SER ASP MET LEU GLU SEQRES 5 A 368 VAL ARG VAL LEU GLY HIS LYS PHE ARG ASN PRO VAL GLY SEQRES 6 A 368 ILE ALA ALA GLY PHE ASP LYS HIS GLY GLU ALA VAL ASP SEQRES 7 A 368 GLY LEU TYR LYS MET GLY PHE GLY PHE VAL GLU ILE GLY SEQRES 8 A 368 SER VAL THR PRO LYS PRO GLN GLU GLY ASN PRO ARG PRO SEQRES 9 A 368 ARG VAL PHE ARG LEU PRO GLU ASP GLN ALA VAL ILE ASN SEQRES 10 A 368 ARG TYR GLY PHE ASN SER HIS GLY LEU SER VAL VAL GLU SEQRES 11 A 368 HIS ARG LEU ARG ALA ARG GLN GLN LYS GLN ALA LYS LEU SEQRES 12 A 368 THR GLU ASP GLY LEU PRO LEU GLY VAL ASN LEU GLY LYS SEQRES 13 A 368 ASN LYS THR SER VAL ASP ALA ALA GLU ASP TYR ALA GLU SEQRES 14 A 368 GLY VAL ARG VAL LEU GLY PRO LEU ALA ASP TYR LEU VAL SEQRES 15 A 368 VAL ASN VAL SER SER PRO ASN THR ALA GLY LEU ARG SER SEQRES 16 A 368 LEU GLN GLY LYS ALA GLU LEU ARG ARG LEU LEU THR LYS SEQRES 17 A 368 VAL LEU GLN GLU ARG ASP GLY LEU ARG ARG VAL HIS ARG SEQRES 18 A 368 PRO ALA VAL LEU VAL LYS ILE ALA PRO ASP LEU THR SER SEQRES 19 A 368 GLN ASP LYS GLU ASP ILE ALA SER VAL VAL LYS GLU LEU SEQRES 20 A 368 GLY ILE ASP GLY LEU ILE VAL THR ASN THR THR VAL SER SEQRES 21 A 368 ARG PRO ALA GLY LEU GLN GLY ALA LEU ARG SER GLU THR SEQRES 22 A 368 GLY GLY LEU SER GLY LYS PRO LEU ARG ASP LEU SER THR SEQRES 23 A 368 GLN THR ILE ARG GLU MET TYR ALA LEU THR GLN GLY ARG SEQRES 24 A 368 VAL PRO ILE ILE GLY VAL GLY GLY VAL SER SER GLY GLN SEQRES 25 A 368 ASP ALA LEU GLU LYS ILE ARG ALA GLY ALA SER LEU VAL SEQRES 26 A 368 GLN LEU TYR THR ALA LEU THR PHE TRP GLY PRO PRO VAL SEQRES 27 A 368 VAL GLY LYS VAL LYS ARG GLU LEU GLU ALA LEU LEU LYS SEQRES 28 A 368 GLU GLN GLY PHE GLY GLY VAL THR ASP ALA ILE GLY ALA SEQRES 29 A 368 ASP HIS ARG ARG HET FNR A 400 52 HET ORO A 401 14 HET CE9 A 402 72 HET SO4 A 403 5 HET SO4 A 404 5 HET ACT A 405 7 HET ACT A 406 14 HET ACT A 407 14 HET CL A 408 1 HET CL A 409 1 HET CL A 410 1 HET GOL A 411 14 HETNAM FNR 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H- HETNAM 2 FNR BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D- HETNAM 3 FNR RIBITOL HETNAM ORO OROTIC ACID HETNAM CE9 DODECYL NONA ETHYLENE GLYCOL ETHER HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETSYN FNR TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE HETSYN CE9 POLYDOCANOL; THESIT HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FNR C17 H23 N4 O9 P FORMUL 3 ORO C5 H4 N2 O4 FORMUL 4 CE9 C30 H62 O10 FORMUL 5 SO4 2(O4 S 2-) FORMUL 7 ACT 3(C2 H3 O2 1-) FORMUL 10 CL 3(CL 1-) FORMUL 13 GOL C3 H8 O3 FORMUL 14 HOH *395(H2 O) HELIX 1 AA1 LEU A 42 LEU A 50 1 9 HELIX 2 AA2 ASP A 51 LEU A 65 1 15 HELIX 3 AA3 SER A 76 GLU A 80 5 5 HELIX 4 AA4 ALA A 104 MET A 111 1 8 HELIX 5 AA5 PRO A 138 ASP A 140 5 3 HELIX 6 AA6 GLY A 153 ALA A 163 1 11 HELIX 7 AA7 ARG A 164 ASP A 174 1 11 HELIX 8 AA8 ASP A 190 GLY A 203 1 14 HELIX 9 AA9 PRO A 204 ALA A 206 5 3 HELIX 10 AB1 GLY A 220 GLN A 225 5 6 HELIX 11 AB2 GLY A 226 GLY A 243 1 18 HELIX 12 AB3 ARG A 245 ARG A 249 5 5 HELIX 13 AB4 THR A 261 GLY A 276 1 16 HELIX 14 AB5 LEU A 309 THR A 324 1 16 HELIX 15 AB6 SER A 338 GLY A 349 1 12 HELIX 16 AB7 TYR A 356 GLY A 363 1 8 HELIX 17 AB8 PRO A 364 GLN A 381 1 18 HELIX 18 AB9 GLY A 385 ILE A 390 1 6 HELIX 19 AC1 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 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 ALA A 350 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 7.11 CISPEP 2 ARG A 131 PRO A 132 0 3.14 CISPEP 3 VAL A 282 THR A 283 0 10.62 SITE 1 AC1 26 ALA A 95 ALA A 96 GLY A 97 LYS A 100 SITE 2 AC1 26 GLY A 119 SER A 120 ASN A 145 TYR A 147 SITE 3 AC1 26 ASN A 181 ASN A 212 LYS A 255 THR A 283 SITE 4 AC1 26 ASN A 284 THR A 285 SER A 305 GLY A 306 SITE 5 AC1 26 LEU A 309 VAL A 333 GLY A 334 GLY A 335 SITE 6 AC1 26 LEU A 355 TYR A 356 THR A 357 ORO A 401 SITE 7 AC1 26 HOH A 551 HOH A 576 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 FNR A 400 SITE 1 AC3 8 MET A 43 LEU A 46 ALA A 55 HIS A 56 SITE 2 AC3 8 ALA A 59 THR A 63 THR A 360 HOH A 731 SITE 1 AC4 4 ARG A 245 VAL A 247 HIS A 248 HOH A 515 SITE 1 AC5 2 ARG A 249 HOH A 680 SITE 1 AC6 9 GLN A 168 ALA A 169 THR A 172 LEU A 205 SITE 2 AC6 9 ALA A 206 ASP A 207 HOH A 513 HOH A 630 SITE 3 AC6 9 HOH A 692 SITE 1 AC7 2 ARG A 160 HOH A 739 SITE 1 AC8 6 ASP A 311 THR A 314 GLN A 315 ARG A 318 SITE 2 AC8 6 GLU A 344 HOH A 543 SITE 1 AC9 5 GLN A 165 PRO A 204 HIS A 248 ARG A 298 SITE 2 AC9 5 SER A 299 SITE 1 AD1 4 ARG A 347 GLN A 381 HOH A 535 HOH A 558 SITE 1 AD2 5 ARG A 245 THR A 301 GLY A 302 HOH A 676 SITE 2 AD2 5 HOH A 804 SITE 1 AD3 3 SER A 155 HOH A 651 HOH A 837 CRYST1 90.140 90.140 122.152 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 0.011094 0.006405 0.000000 0.00000 SCALE2 0.000000 0.012810 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008187 0.00000