HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 04-JAN-19 6J3B TITLE CRYSTAL STRUCTURE OF HUMAN DHODH IN COMPLEX WITH INHIBITOR 1289 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DHODEHASE,DIHYDROOROTATE OXIDASE; COMPND 5 EC: 1.3.5.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DHODH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DHODH, INHIBITOR, COMPLEX, OXIDOREDUCTASE, OXIDOREDUCTASE- KEYWDS 2 OXIDOREDUCTASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.YU,Q.CHEN REVDAT 2 27-MAR-24 6J3B 1 REMARK REVDAT 1 21-AUG-19 6J3B 0 JRNL AUTH T.ZENG,Z.ZUO,Y.LUO,Y.ZHAO,Y.YU,Q.CHEN JRNL TITL A NOVEL SERIES OF HUMAN DIHYDROOROTATE DEHYDROGENASE JRNL TITL 2 INHIBITORS DISCOVERED BY IN VITRO SCREENING: INHIBITION JRNL TITL 3 ACTIVITY AND CRYSTALLOGRAPHIC BINDING MODE. JRNL REF FEBS OPEN BIO V. 9 1348 2019 JRNL REFN ESSN 2211-5463 JRNL PMID 31087527 JRNL DOI 10.1002/2211-5463.12658 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 77356 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 3835 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 48.4115 - 4.7973 0.99 2896 152 0.1910 0.2269 REMARK 3 2 4.7973 - 3.8083 1.00 2814 148 0.1418 0.1833 REMARK 3 3 3.8083 - 3.3270 1.00 2741 178 0.1367 0.1527 REMARK 3 4 3.3270 - 3.0229 1.00 2750 165 0.1411 0.1535 REMARK 3 5 3.0229 - 2.8062 1.00 2750 167 0.1406 0.1521 REMARK 3 6 2.8062 - 2.6408 1.00 2714 156 0.1435 0.1571 REMARK 3 7 2.6408 - 2.5085 1.00 2759 139 0.1394 0.1666 REMARK 3 8 2.5085 - 2.3994 1.00 2711 153 0.1379 0.1590 REMARK 3 9 2.3994 - 2.3070 1.00 2769 120 0.1337 0.1549 REMARK 3 10 2.3070 - 2.2274 1.00 2733 127 0.1328 0.1601 REMARK 3 11 2.2274 - 2.1577 1.00 2716 144 0.1419 0.1574 REMARK 3 12 2.1577 - 2.0961 1.00 2715 136 0.1500 0.1656 REMARK 3 13 2.0961 - 2.0409 1.00 2731 144 0.1563 0.1621 REMARK 3 14 2.0409 - 1.9911 1.00 2730 130 0.1554 0.1584 REMARK 3 15 1.9911 - 1.9458 1.00 2728 132 0.1602 0.1957 REMARK 3 16 1.9458 - 1.9044 1.00 2673 157 0.1584 0.1682 REMARK 3 17 1.9044 - 1.8663 1.00 2721 139 0.1651 0.1663 REMARK 3 18 1.8663 - 1.8311 1.00 2699 139 0.1687 0.1818 REMARK 3 19 1.8311 - 1.7984 1.00 2722 125 0.1838 0.2332 REMARK 3 20 1.7984 - 1.7679 1.00 2709 127 0.1834 0.2176 REMARK 3 21 1.7679 - 1.7394 1.00 2700 148 0.1909 0.2276 REMARK 3 22 1.7394 - 1.7126 1.00 2671 135 0.1992 0.2175 REMARK 3 23 1.7126 - 1.6874 1.00 2721 129 0.1958 0.2230 REMARK 3 24 1.6874 - 1.6637 1.00 2714 119 0.2085 0.1922 REMARK 3 25 1.6637 - 1.6412 0.99 2675 148 0.2107 0.2430 REMARK 3 26 1.6412 - 1.6199 0.98 2666 122 0.2222 0.2317 REMARK 3 27 1.6199 - 1.5996 0.96 2593 156 0.2425 0.2511 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 3116 REMARK 3 ANGLE : 1.087 4234 REMARK 3 CHIRALITY : 0.040 457 REMARK 3 PLANARITY : 0.006 557 REMARK 3 DIHEDRAL : 15.023 1169 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6J3B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1300010393. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77757 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES PH4.6, 2M AMMONIUM SULPHATE, 30% REMARK 280 GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 81.83600 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 40.91800 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 40.91800 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 81.83600 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: 220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 826 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 O HOH A 508 O HOH A 688 2.02 REMARK 500 O4 SO4 A 416 O HOH A 501 2.04 REMARK 500 O HOH A 507 O HOH A 524 2.05 REMARK 500 OE1 GLU A 319 O HOH A 502 2.07 REMARK 500 O HOH A 616 O HOH A 699 2.11 REMARK 500 O ASN A 212 O HOH A 503 2.14 REMARK 500 O HOH A 506 O HOH A 740 2.17 REMARK 500 CL CL A 420 O HOH A 687 2.18 REMARK 500 OE1 GLU A 266 O HOH A 504 2.18 REMARK 500 O HOH A 557 O HOH A 744 2.18 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 502 O HOH A 610 6554 2.09 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 -56.39 -124.27 REMARK 500 PHE A 73 108.50 -55.33 REMARK 500 ASP A 99 79.60 -112.03 REMARK 500 ARG A 133 11.06 -142.63 REMARK 500 ARG A 133 10.73 -142.63 REMARK 500 LEU A 137 78.17 -117.89 REMARK 500 SER A 337 10.83 -142.22 REMARK 500 TYR A 356 -62.62 -143.84 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 826 DISTANCE = 6.22 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 422 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 267 OD2 REMARK 620 2 HOH A 527 O 109.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 423 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 354 O REMARK 620 2 FMN A 403 O2P 112.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ORO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue B5O A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LDA A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 418 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 419 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 420 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 421 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 422 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 423 DBREF 6J3B A 31 396 UNP Q02127 PYRD_HUMAN 30 395 SEQRES 1 A 366 ALA THR GLY ASP GLU ARG PHE TYR ALA GLU HIS LEU MET SEQRES 2 A 366 PRO THR LEU GLN GLY LEU LEU ASP PRO GLU SER ALA HIS SEQRES 3 A 366 ARG LEU ALA VAL ARG PHE THR SER LEU GLY LEU LEU PRO SEQRES 4 A 366 ARG ALA ARG PHE GLN ASP SER ASP MET LEU GLU VAL ARG SEQRES 5 A 366 VAL LEU GLY HIS LYS PHE ARG ASN PRO VAL GLY ILE ALA SEQRES 6 A 366 ALA GLY PHE ASP LYS HIS GLY GLU ALA VAL ASP GLY LEU SEQRES 7 A 366 TYR LYS MET GLY PHE GLY PHE VAL GLU ILE GLY SER VAL SEQRES 8 A 366 THR PRO LYS PRO GLN GLU GLY ASN PRO ARG PRO ARG VAL SEQRES 9 A 366 PHE ARG LEU PRO GLU ASP GLN ALA VAL ILE ASN ARG TYR SEQRES 10 A 366 GLY PHE ASN SER HIS GLY LEU SER VAL VAL GLU HIS ARG SEQRES 11 A 366 LEU ARG ALA ARG GLN GLN LYS GLN ALA LYS LEU THR GLU SEQRES 12 A 366 ASP GLY LEU PRO LEU GLY VAL ASN LEU GLY LYS ASN LYS SEQRES 13 A 366 THR SER VAL ASP ALA ALA GLU ASP TYR ALA GLU GLY VAL SEQRES 14 A 366 ARG VAL LEU GLY PRO LEU ALA ASP TYR LEU VAL VAL ASN SEQRES 15 A 366 VAL SER SER PRO ASN THR ALA GLY LEU ARG SER LEU GLN SEQRES 16 A 366 GLY LYS ALA GLU LEU ARG ARG LEU LEU THR LYS VAL LEU SEQRES 17 A 366 GLN GLU ARG ASP GLY LEU ARG ARG VAL HIS ARG PRO ALA SEQRES 18 A 366 VAL LEU VAL LYS ILE ALA PRO ASP LEU THR SER GLN ASP SEQRES 19 A 366 LYS GLU ASP ILE ALA SER VAL VAL LYS GLU LEU GLY ILE SEQRES 20 A 366 ASP GLY LEU ILE VAL THR ASN THR THR VAL SER ARG PRO SEQRES 21 A 366 ALA GLY LEU GLN GLY ALA LEU ARG SER GLU THR GLY GLY SEQRES 22 A 366 LEU SER GLY LYS PRO LEU ARG ASP LEU SER THR GLN THR SEQRES 23 A 366 ILE ARG GLU MET TYR ALA LEU THR GLN GLY ARG VAL PRO SEQRES 24 A 366 ILE ILE GLY VAL GLY GLY VAL SER SER GLY GLN ASP ALA SEQRES 25 A 366 LEU GLU LYS ILE ARG ALA GLY ALA SER LEU VAL GLN LEU SEQRES 26 A 366 TYR THR ALA LEU THR PHE TRP GLY PRO PRO VAL VAL GLY SEQRES 27 A 366 LYS VAL LYS ARG GLU LEU GLU ALA LEU LEU LYS GLU GLN SEQRES 28 A 366 GLY PHE GLY GLY VAL THR ASP ALA ILE GLY ALA ASP HIS SEQRES 29 A 366 ARG ARG HET SO4 A 401 5 HET SO4 A 402 5 HET FMN A 403 50 HET ORO A 404 11 HET B5O A 405 50 HET LDA A 406 47 HET DMS A 407 10 HET DMS A 408 10 HET ACT A 409 7 HET ACT A 410 7 HET ACT A 411 7 HET ACT A 412 7 HET ACT A 413 7 HET ACT A 414 7 HET SO4 A 415 5 HET SO4 A 416 5 HET SO4 A 417 5 HET SO4 A 418 5 HET CL A 419 1 HET CL A 420 1 HET CL A 421 1 HET NA A 422 1 HET NA A 423 1 HETNAM SO4 SULFATE ION HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM ORO OROTIC ACID HETNAM B5O (6R)-1-[3,5-BIS(FLUORANYL)-4-[2-FLUORANYL-5- HETNAM 2 B5O (HYDROXYMETHYL)PHENYL]PHENYL]-6-PROPAN-2-YL-6,7- HETNAM 3 B5O DIHYDRO-5H-BENZOTRIAZOL-4-ONE HETNAM LDA LAURYL DIMETHYLAMINE-N-OXIDE HETNAM DMS DIMETHYL SULFOXIDE HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 SO4 6(O4 S 2-) FORMUL 4 FMN C17 H21 N4 O9 P FORMUL 5 ORO C5 H4 N2 O4 FORMUL 6 B5O C22 H20 F3 N3 O2 FORMUL 7 LDA C14 H31 N O FORMUL 8 DMS 2(C2 H6 O S) FORMUL 10 ACT 6(C2 H3 O2 1-) FORMUL 20 CL 3(CL 1-) FORMUL 23 NA 2(NA 1+) FORMUL 25 HOH *326(H2 O) HELIX 1 AA1 THR A 32 HIS A 41 1 10 HELIX 2 AA2 HIS A 41 LEU A 50 1 10 HELIX 3 AA3 ASP A 51 LEU A 65 1 15 HELIX 4 AA4 SER A 76 GLU A 80 5 5 HELIX 5 AA5 ALA A 104 MET A 111 1 8 HELIX 6 AA6 PRO A 138 ASP A 140 5 3 HELIX 7 AA7 GLY A 153 ALA A 163 1 11 HELIX 8 AA8 ARG A 164 ASP A 174 1 11 HELIX 9 AA9 ASP A 190 GLY A 203 1 14 HELIX 10 AB1 PRO A 204 ALA A 206 5 3 HELIX 11 AB2 GLY A 220 GLN A 225 5 6 HELIX 12 AB3 GLY A 226 GLY A 243 1 18 HELIX 13 AB4 ARG A 245 ARG A 249 5 5 HELIX 14 AB5 THR A 261 GLY A 276 1 16 HELIX 15 AB6 LEU A 309 THR A 324 1 16 HELIX 16 AB7 SER A 338 GLY A 349 1 12 HELIX 17 AB8 TYR A 356 GLY A 363 1 8 HELIX 18 AB9 PRO A 365 GLN A 381 1 17 HELIX 19 AC1 GLY A 385 ILE A 390 1 6 HELIX 20 AC2 GLY A 391 ARG A 396 5 6 SHEET 1 AA1 2 VAL A 81 VAL A 83 0 SHEET 2 AA1 2 HIS A 86 PHE A 88 -1 O PHE A 88 N VAL A 81 SHEET 1 AA2 9 VAL A 92 ILE A 94 0 SHEET 2 AA2 9 PHE A 115 VAL A 121 1 O PHE A 115 N ILE A 94 SHEET 3 AA2 9 LEU A 178 LEU A 182 1 O GLY A 179 N VAL A 116 SHEET 4 AA2 9 TYR A 208 ASN A 212 1 O VAL A 210 N LEU A 182 SHEET 5 AA2 9 ALA A 251 ILE A 256 1 O LEU A 253 N VAL A 211 SHEET 6 AA2 9 GLY A 279 VAL A 282 1 O ILE A 281 N 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 LEU A 352 LEU A 355 1 O LEU A 352 N GLY A 332 SHEET 9 AA2 9 VAL A 92 ILE A 94 1 N GLY A 93 O VAL A 353 SHEET 1 AA3 3 VAL A 134 LEU A 137 0 SHEET 2 AA3 3 ALA A 142 ASN A 145 -1 O ALA A 142 N LEU A 137 SHEET 3 AA3 3 GLY A 303 GLY A 306 -1 O GLY A 303 N ASN A 145 LINK OD2 ASP A 267 NA NA A 422 1555 1555 2.58 LINK O GLN A 354 NA NA A 423 1555 1555 2.72 LINK O2P FMN A 403 NA NA A 423 1555 1555 2.68 LINK NA NA A 422 O HOH A 527 1555 1555 2.82 CISPEP 1 GLY A 119 SER A 120 0 5.82 CISPEP 2 ARG A 131 PRO A 132 0 3.17 CISPEP 3 VAL A 282 THR A 283 0 11.89 SITE 1 AC1 6 ARG A 245 VAL A 247 HIS A 248 HOH A 578 SITE 2 AC1 6 HOH A 625 HOH A 714 SITE 1 AC2 6 ALA A 219 GLY A 220 ARG A 222 HOH A 509 SITE 2 AC2 6 HOH A 537 HOH A 621 SITE 1 AC3 25 ALA A 95 ALA A 96 GLY A 97 LYS A 100 SITE 2 AC3 25 SER A 120 ASN A 145 TYR A 147 ASN A 181 SITE 3 AC3 25 ASN A 212 LYS A 255 THR A 283 ASN A 284 SITE 4 AC3 25 THR A 285 SER A 305 GLY A 306 LEU A 309 SITE 5 AC3 25 VAL A 333 GLY A 334 GLY A 335 LEU A 355 SITE 6 AC3 25 TYR A 356 THR A 357 ORO A 404 NA A 423 SITE 7 AC3 25 HOH A 591 SITE 1 AC4 11 LYS A 100 ASN A 145 TYR A 147 GLY A 148 SITE 2 AC4 11 PHE A 149 ASN A 212 SER A 215 ASN A 217 SITE 3 AC4 11 ASN A 284 THR A 285 FMN A 403 SITE 1 AC5 14 TYR A 38 MET A 43 LEU A 46 GLN A 47 SITE 2 AC5 14 PRO A 52 ALA A 55 HIS A 56 ALA A 59 SITE 3 AC5 14 THR A 63 LEU A 67 ARG A 136 TYR A 356 SITE 4 AC5 14 LEU A 359 THR A 360 SITE 1 AC6 16 PRO A 138 ASP A 140 GLN A 141 PRO A 290 SITE 2 AC6 16 LYS A 307 PRO A 308 ASP A 311 GLN A 315 SITE 3 AC6 16 ARG A 318 GLU A 344 ARG A 347 ASP A 393 SITE 4 AC6 16 HOH A 645 HOH A 674 HOH A 681 HOH A 685 SITE 1 AC7 4 LYS A 170 THR A 261 GLN A 263 HOH A 538 SITE 1 AC8 2 SER A 262 HOH A 538 SITE 1 AC9 9 GLN A 168 ALA A 169 THR A 172 LEU A 205 SITE 2 AC9 9 ALA A 206 ASP A 207 SO4 A 416 HOH A 511 SITE 3 AC9 9 HOH A 646 SITE 1 AD1 3 GLU A 127 ASN A 129 HOH A 678 SITE 1 AD2 3 LYS A 124 SER A 155 HOH A 794 SITE 1 AD3 2 ARG A 160 HOH A 773 SITE 1 AD4 2 LYS A 227 ARG A 231 SITE 1 AD5 7 ALA A 71 ARG A 72 PHE A 73 HOH A 534 SITE 2 AD5 7 HOH A 628 HOH A 664 HOH A 744 SITE 1 AD6 2 ARG A 249 HOH A 522 SITE 1 AD7 9 HIS A 86 ALA A 206 ASP A 207 ARG A 246 SITE 2 AD7 9 VAL A 247 ARG A 249 ACT A 409 HOH A 501 SITE 3 AD7 9 HOH A 540 SITE 1 AD8 7 ARG A 57 HIS A 101 ASN A 150 HIS A 152 SITE 2 AD8 7 HOH A 535 HOH A 608 HOH A 649 SITE 1 AD9 10 SER A 262 LYS A 265 ALA A 291 GLY A 292 SITE 2 AD9 10 GLU A 319 HOH A 530 HOH A 553 HOH A 554 SITE 3 AD9 10 HOH A 559 HOH A 661 SITE 1 AE1 5 GLN A 165 HIS A 248 ARG A 298 SER A 299 SITE 2 AE1 5 CL A 420 SITE 1 AE2 6 ARG A 162 GLN A 165 LEU A 205 ARG A 298 SITE 2 AE2 6 CL A 419 HOH A 687 SITE 1 AE3 5 ARG A 245 THR A 301 GLY A 302 HOH A 662 SITE 2 AE3 5 HOH A 771 SITE 1 AE4 4 GLY A 226 LYS A 227 ASP A 267 HOH A 527 SITE 1 AE5 6 GLY A 334 GLY A 335 VAL A 336 GLN A 354 SITE 2 AE5 6 LEU A 355 FMN A 403 CRYST1 90.829 90.829 122.754 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 0.011010 0.006356 0.000000 0.00000 SCALE2 0.000000 0.012713 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008146 0.00000