HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 31-MAY-16 5K9C TITLE CRYSTAL STRUCTURE OF HUMAN DIHYDROOROTATE DEHYDROGENASE WITH ML390 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_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS OXIDOREDUCTASE, ALPHA/BETA BARREL, INHIBITOR, OXIDOREDUCTASE- KEYWDS 2 OXIDOREDUCTASE INHIBITOR COMPLEX 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 5K9C 1 REMARK REVDAT 2 04-JAN-17 5K9C 1 JRNL REVDAT 1 12-OCT-16 5K9C 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. 1.66 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) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 67468 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 3227 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 25.9551 - 4.7119 1.00 2971 163 0.1821 0.2052 REMARK 3 2 4.7119 - 3.7436 1.00 2897 144 0.1326 0.1494 REMARK 3 3 3.7436 - 3.2714 1.00 2859 131 0.1271 0.1538 REMARK 3 4 3.2714 - 2.9728 1.00 2812 156 0.1256 0.1351 REMARK 3 5 2.9728 - 2.7600 1.00 2792 173 0.1224 0.1340 REMARK 3 6 2.7600 - 2.5974 1.00 2824 112 0.1251 0.1507 REMARK 3 7 2.5974 - 2.4674 1.00 2801 158 0.1192 0.1525 REMARK 3 8 2.4674 - 2.3601 1.00 2780 139 0.1181 0.1288 REMARK 3 9 2.3601 - 2.2693 1.00 2820 147 0.1136 0.1367 REMARK 3 10 2.2693 - 2.1910 1.00 2769 119 0.1094 0.1210 REMARK 3 11 2.1910 - 2.1226 1.00 2819 152 0.1091 0.1298 REMARK 3 12 2.1226 - 2.0619 1.00 2752 157 0.1147 0.1226 REMARK 3 13 2.0619 - 2.0076 1.00 2823 123 0.1171 0.1252 REMARK 3 14 2.0076 - 1.9587 1.00 2778 129 0.1165 0.1405 REMARK 3 15 1.9587 - 1.9142 1.00 2761 157 0.1251 0.1479 REMARK 3 16 1.9142 - 1.8734 1.00 2738 150 0.1332 0.1428 REMARK 3 17 1.8734 - 1.8360 1.00 2803 143 0.1358 0.1490 REMARK 3 18 1.8360 - 1.8013 1.00 2730 143 0.1362 0.1570 REMARK 3 19 1.8013 - 1.7692 1.00 2820 116 0.1386 0.1517 REMARK 3 20 1.7692 - 1.7392 1.00 2746 145 0.1362 0.1800 REMARK 3 21 1.7392 - 1.7111 0.99 2744 162 0.1474 0.1507 REMARK 3 22 1.7111 - 1.6848 0.98 2766 104 0.1606 0.1659 REMARK 3 23 1.6848 - 1.6600 0.95 2636 104 0.1751 0.2145 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.56 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 : 0.010 2986 REMARK 3 ANGLE : 1.098 4074 REMARK 3 CHIRALITY : 0.074 454 REMARK 3 PLANARITY : 0.008 533 REMARK 3 DIHEDRAL : 14.357 1118 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 35 THROUGH 76 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.2632 -46.5998 119.8611 REMARK 3 T TENSOR REMARK 3 T11: 0.1940 T22: 0.3141 REMARK 3 T33: 0.2411 T12: -0.0108 REMARK 3 T13: -0.0313 T23: -0.0437 REMARK 3 L TENSOR REMARK 3 L11: 0.1769 L22: 0.0450 REMARK 3 L33: 0.4049 L12: -0.0891 REMARK 3 L13: -0.0862 L23: 0.0378 REMARK 3 S TENSOR REMARK 3 S11: 0.0629 S12: 0.2829 S13: -0.3095 REMARK 3 S21: -0.0157 S22: -0.0775 S23: 0.0987 REMARK 3 S31: 0.2651 S32: -0.2775 S33: -0.0180 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 77 THROUGH 94 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.1814 -54.0039 140.3249 REMARK 3 T TENSOR REMARK 3 T11: 0.1565 T22: 0.1337 REMARK 3 T33: 0.1439 T12: 0.0091 REMARK 3 T13: 0.0590 T23: 0.0366 REMARK 3 L TENSOR REMARK 3 L11: 0.1041 L22: 0.0137 REMARK 3 L33: 0.1114 L12: 0.0174 REMARK 3 L13: 0.0940 L23: -0.0012 REMARK 3 S TENSOR REMARK 3 S11: -0.0931 S12: -0.0859 S13: -0.1379 REMARK 3 S21: 0.1365 S22: -0.0044 S23: 0.1067 REMARK 3 S31: 0.0832 S32: -0.0081 S33: -0.0222 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 95 THROUGH 396 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.6612 -39.9650 134.0486 REMARK 3 T TENSOR REMARK 3 T11: 0.0482 T22: 0.0935 REMARK 3 T33: 0.0705 T12: 0.0068 REMARK 3 T13: 0.0022 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.7218 L22: 0.3789 REMARK 3 L33: 0.7664 L12: -0.2126 REMARK 3 L13: -0.4308 L23: 0.2135 REMARK 3 S TENSOR REMARK 3 S11: 0.0089 S12: -0.0803 S13: 0.0042 REMARK 3 S21: 0.0058 S22: -0.0060 S23: 0.0301 REMARK 3 S31: 0.0123 S32: 0.0160 S33: -0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE AUTHORS STATE THAT ELECTRON DENSITY REMARK 3 ANALYSIS REVEALED THAT THE MAIN CHAIN HAD A DOUBLE CONFORMATION REMARK 3 ( FROM RESIDUE 211 TO 226), DUE TO ITS EXPECTED FLEXIBILITY (AS REMARK 3 A CATALYTIC LOOP). VAL213 SHOWED A VERY CLEAR ELECTRON DENSITY REMARK 3 IN CONFORMATION B, BUT IN CONTRAST, CONFORMATION A WAS DOMINANT REMARK 3 FOR RESIDUES FROM 214 TO 218. THE VAL213 CONFORMER AND THE REMARK 3 SER214 A CONFORMER WERE CONFLICTING AS A CONSEQUENCE OF THE REMARK 3 DIFFERENT LOOP ARRANGEMENTS (OPEN AND CLOSED CONFORMATIONS). REMARK 3 TAKING ALL THESE INTO ACCOUNT, THE AUTHORS STATE THAT THE VAL213 REMARK 3 DOUBLE CONFORMATION IS THE SOLUTION THAT BETTER FITS THE DATASET REMARK 3 AND THEREFORE, VAL213 (B CONFORMER) AND SER214 (A CONFORMER) ARE REMARK 3 NOT LINKED. REMARK 4 REMARK 4 5K9C 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_1000221888. 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) : 1.4586 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 : 67579 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 25.952 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 15.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09700 REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.40700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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 (%): 64.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.8 REMARK 280 1.9 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 81.18067 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 40.59033 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 40.59033 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 81.18067 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 840 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 ALA A 219 REMARK 465 GLY A 220 REMARK 465 LEU A 221 REMARK 465 ARG A 222 REMARK 465 SER A 223 REMARK 465 LEU A 224 REMARK 465 GLN A 225 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 ARG A 36 CG CD NE CZ NH1 NH2 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 LEU A 46 CG CD1 CD2 REMARK 470 LEU A 49 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 NE CZ NH1 NH2 REMARK 470 ARG A 396 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 728 O HOH A 758 1.88 REMARK 500 O HOH A 760 O HOH A 802 1.89 REMARK 500 O HOH A 786 O HOH A 795 1.98 REMARK 500 O HOH A 666 O HOH A 758 1.99 REMARK 500 O HOH A 711 O HOH A 756 2.00 REMARK 500 O HOH A 716 O HOH A 730 2.00 REMARK 500 O HOH A 747 O HOH A 760 2.02 REMARK 500 O HOH A 672 O HOH A 752 2.06 REMARK 500 O HOH A 515 O HOH A 787 2.09 REMARK 500 O HOH A 726 O HOH A 787 2.11 REMARK 500 O HOH A 748 O HOH A 753 2.13 REMARK 500 O HOH A 738 O HOH A 764 2.13 REMARK 500 O HOH A 692 O HOH A 753 2.14 REMARK 500 O HOH A 741 O HOH A 832 2.15 REMARK 500 O HOH A 637 O HOH A 718 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 606 O HOH A 757 5547 1.80 REMARK 500 O HOH A 646 O HOH A 828 2544 2.14 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 ASP A 99 79.46 -105.38 REMARK 500 ARG A 133 12.77 -142.82 REMARK 500 ASP A 190 84.82 -156.65 REMARK 500 TYR A 356 -64.84 -144.14 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 840 DISTANCE = 6.66 ANGSTROMS 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 MLJ 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 GOL A 410 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5K9D RELATED DB: PDB DBREF 5K9C A 30 396 UNP Q02127 PYRD_HUMAN 29 395 SEQADV 5K9C 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 MLJ A 402 100 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 GOL A 410 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 MLJ ~{N}-[3-OXIDANYLIDENE-3-[[(1~{R})-1,2,3,4- HETNAM 2 MLJ TETRAHYDRONAPHTHALEN-1-YL]AMINO]PROPYL]-4- HETNAM 3 MLJ (TRIFLUOROMETHYLOXY)BENZAMIDE HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETSYN FNR TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE 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 MLJ C21 H21 F3 N2 O3 FORMUL 5 SO4 2(O4 S 2-) FORMUL 7 ACT 3(C2 H3 O2 1-) FORMUL 10 CL 2(CL 1-) FORMUL 12 GOL C3 H8 O3 FORMUL 13 HOH *340(H2 O) HELIX 1 AA1 GLU A 35 HIS A 41 1 7 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 LYS A 227 GLY A 243 1 17 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 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 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 4.84 CISPEP 2 ARG A 131 PRO A 132 0 5.36 CISPEP 3 VAL A 282 THR A 283 0 11.72 SITE 1 AC1 25 ALA A 95 ALA A 96 GLY A 97 LYS A 100 SITE 2 AC1 25 GLY A 119 SER A 120 ASN A 145 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 401 HOH A 534 SITE 7 AC1 25 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 16 MET A 43 LEU A 46 GLN A 47 LEU A 50 SITE 2 AC3 16 PRO A 52 ALA A 55 HIS A 56 LEU A 58 SITE 3 AC3 16 ALA A 59 PHE A 62 PHE A 98 VAL A 134 SITE 4 AC3 16 ARG A 136 TYR A 356 THR A 360 PHE A 361 SITE 1 AC4 4 ARG A 245 VAL A 247 HIS A 248 HOH A 550 SITE 1 AC5 2 ARG A 249 HOH A 546 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 511 HOH A 569 SITE 3 AC6 9 HOH A 581 SITE 1 AC7 8 LYS A 307 PRO A 308 ASP A 311 THR A 314 SITE 2 AC7 8 GLN A 315 ARG A 318 HOH A 552 HOH A 561 SITE 1 AC8 5 ARG A 160 HOH A 577 HOH A 635 HOH A 637 SITE 2 AC8 5 HOH A 689 SITE 1 AC9 5 GLN A 165 HIS A 248 ARG A 298 SER A 299 SITE 2 AC9 5 HOH A 659 SITE 1 AD1 3 ARG A 347 GLN A 381 HOH A 523 SITE 1 AD2 4 LYS A 167 LYS A 227 ARG A 231 HOH A 520 CRYST1 89.900 89.900 121.771 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 0.011123 0.006422 0.000000 0.00000 SCALE2 0.000000 0.012844 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008212 0.00000