HEADER HYDROLASE 09-JUN-23 8PBT TITLE MUTANT K1482M OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD PROTEIN BOUND TITLE 2 TO THE SUBSTRATE DIHYDROOROTATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAD PROTEIN; COMPND 3 CHAIN: A; COMPND 4 EC: 6.3.5.5,2.1.3.2,3.5.2.3; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CAD; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293S GNTI; SOURCE 9 EXPRESSION_SYSTEM_ATCC_NUMBER: CRL-3022; SOURCE 10 EXPRESSION_SYSTEM_ORGAN: EMBRYO; SOURCE 11 EXPRESSION_SYSTEM_TISSUE: KIDNEY; SOURCE 12 EXPRESSION_SYSTEM_CELL: EPITHELIAL-LIKE; SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: POPIN-M-HUDHO-K1482M KEYWDS NUCLEOTIDE METABOLISM, DE NOVO PYRIMIDINE SYNTHESIS, CAD DISEASE, KEYWDS 2 MULTIENZYMATIC PROTEIN, ZINC, CARBOXYLATED LYSINE, BIOSYNTHETIC KEYWDS 3 PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.DEL CANO-OCHOA,S.RAMON-MAIQUES REVDAT 3 22-NOV-23 8PBT 1 JRNL REVDAT 2 15-NOV-23 8PBT 1 REMARK REVDAT 1 01-NOV-23 8PBT 0 JRNL AUTH F.DEL CANO-OCHOA,B.G.NG,A.RUBIO-DEL-CAMPO,S.MAHAJAN, JRNL AUTH 2 M.P.WILSON,M.VILAR,D.RYMEN,P.SANCHEZ-PINTOS,J.KENNY, JRNL AUTH 3 M.LEY MARTOS,T.CAMPOS,S.B.WORTMANN,H.H.FREEZE, JRNL AUTH 4 S.RAMON-MAIQUES JRNL TITL BEYOND GENETICS: DECIPHERING THE IMPACT OF MISSENSE VARIANTS JRNL TITL 2 IN CAD DEFICIENCY. JRNL REF J INHERIT METAB DIS V. 46 1170 2023 JRNL REFN ISSN 1573-2665 JRNL PMID 37540500 JRNL DOI 10.1002/JIMD.12667 REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 79.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.9 REMARK 3 NUMBER OF REFLECTIONS : 64377 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 3200 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 79.3600 - 4.0800 0.99 3178 176 0.1592 0.1563 REMARK 3 2 4.0800 - 3.2400 0.87 2718 130 0.1395 0.1499 REMARK 3 3 3.2400 - 2.8300 0.99 3028 174 0.1532 0.1734 REMARK 3 4 2.8300 - 2.5700 0.60 1848 86 0.1485 0.1781 REMARK 3 5 2.5700 - 2.3900 1.00 3036 183 0.1381 0.1737 REMARK 3 6 2.3900 - 2.2600 0.99 2687 155 0.1244 0.1558 REMARK 3 7 2.2300 - 2.1300 1.00 2721 146 0.1130 0.1427 REMARK 3 8 2.1300 - 2.1000 0.95 955 48 0.1064 0.1615 REMARK 3 9 2.0300 - 1.9600 0.99 2637 131 0.1125 0.1565 REMARK 3 10 1.9600 - 1.8900 0.31 916 56 0.1317 0.1964 REMARK 3 11 1.8900 - 1.8300 0.81 2429 125 0.1427 0.1623 REMARK 3 12 1.8300 - 1.7800 1.00 3015 148 0.1222 0.1458 REMARK 3 13 1.7800 - 1.7400 1.00 3023 137 0.1211 0.1685 REMARK 3 14 1.7400 - 1.6900 0.74 2192 136 0.1241 0.1710 REMARK 3 15 1.6900 - 1.6500 0.97 2888 154 0.1346 0.1650 REMARK 3 16 1.6500 - 1.6200 0.99 2938 176 0.1466 0.1897 REMARK 3 17 1.6200 - 1.5900 0.99 3016 150 0.1669 0.1792 REMARK 3 18 1.5900 - 1.5600 1.00 2991 141 0.1938 0.2259 REMARK 3 19 1.5600 - 1.5300 1.00 3003 134 0.2186 0.3027 REMARK 3 20 1.5300 - 1.5000 0.99 2984 147 0.2317 0.2980 REMARK 3 21 1.5000 - 1.4800 1.00 2996 152 0.2178 0.2597 REMARK 3 22 1.4800 - 1.4600 1.00 2973 142 0.2386 0.2842 REMARK 3 23 1.4600 - 1.4300 1.00 3005 173 0.2485 0.2891 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.026 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.73 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 : 0.008 2939 REMARK 3 ANGLE : 1.068 4018 REMARK 3 CHIRALITY : 0.086 458 REMARK 3 PLANARITY : 0.010 529 REMARK 3 DIHEDRAL : 7.561 416 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 8PBT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292130973. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97926 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 424906 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 79.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.9 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 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 : 1.610 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER V8.0 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES PH 6.5, 2.7 M SODIUM REMARK 280 FORMATE, 2 MM DIHYDROOROTATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.55750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.55750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 41.03350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 79.36000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.03350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 79.36000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.55750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.03350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 79.36000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 30.55750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.03350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 79.36000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -537.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -30.55750 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 C FMT A1913 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2276 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2304 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2306 LIES ON A SPECIAL POSITION. 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 LYS A1460 CG CD CE NZ REMARK 470 ARG A1507 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1561 CG CD OE1 OE2 REMARK 470 PHE A1563 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A1567 CG CD NE CZ NH1 NH2 REMARK 470 ARG A1661 CG CD NE CZ NH1 NH2 REMARK 470 ARG A1667 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1671 CG CD OE1 OE2 REMARK 470 GLU A1693 CG CD OE1 OE2 REMARK 470 SER A1698 OG REMARK 470 ARG A1699 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1755 CG CD OE1 OE2 REMARK 470 LYS A1780 CG CD CE NZ 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 ASN A1505 43.04 -84.48 REMARK 500 ASN A1560 -139.74 -114.82 REMARK 500 THR A1562 -177.20 -171.63 REMARK 500 GLN A1593 -124.59 52.79 REMARK 500 HIS A1614 76.94 22.00 REMARK 500 HIS A1733 -67.96 -145.80 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 A2326 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A2327 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A2328 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A2329 DISTANCE = 7.58 ANGSTROMS REMARK 525 HOH A2330 DISTANCE = 8.01 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 ZN A1905 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1471 ND1 REMARK 620 2 CYS A1613 SG 113.3 REMARK 620 3 GLU A1637 OE2 78.8 114.4 REMARK 620 4 HOH A2124 O 125.1 107.1 116.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1907 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1471 NE2 REMARK 620 2 HIS A1473 NE2 114.1 REMARK 620 3 KCX A1556 OQ2 89.5 92.2 REMARK 620 4 ASP A1686 OD1 84.4 87.7 173.3 REMARK 620 5 HOH A2104 O 115.7 129.9 92.5 92.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1903 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1481 NE2 REMARK 620 2 HIS A1690 ND1 114.1 REMARK 620 3 GLU A1694 OE1 121.4 115.8 REMARK 620 4 FMT A1917 O1 118.5 104.3 75.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1904 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX A1556 OQ1 REMARK 620 2 HIS A1590 ND1 101.8 REMARK 620 3 HIS A1614 NE2 112.6 92.8 REMARK 620 4 HOH A2104 O 105.0 140.8 102.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1906 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1734 NE2 REMARK 620 2 HIS A1741 ND1 25.2 REMARK 620 3 FMT A1914 O2 37.3 12.3 REMARK 620 4 FMT A1914 O1 33.0 11.0 7.8 REMARK 620 5 FMT A1915 O1 34.2 11.0 10.6 15.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1908 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A1753 OD2 REMARK 620 2 HIS A1756 ND1 106.4 REMARK 620 3 HOH A2247 O 96.0 120.3 REMARK 620 4 HOH A2253 O 117.6 100.4 116.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1909 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A1814 O REMARK 620 2 ALA A1816 O 120.7 REMARK 620 3 FMT A1915 O2 95.2 98.7 REMARK 620 4 HOH A2097 O 86.4 87.2 171.8 REMARK 620 5 HOH A2172 O 108.5 130.6 79.9 91.9 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8PBR RELATED DB: PDB REMARK 900 RELATED ID: 8PBS RELATED DB: PDB REMARK 900 RELATED ID: 8PBU RELATED DB: PDB REMARK 900 RELATED ID: 8PBE RELATED DB: PDB REMARK 900 RELATED ID: 8PBG RELATED DB: PDB REMARK 900 RELATED ID: 8PBH RELATED DB: PDB REMARK 900 RELATED ID: 8PBI RELATED DB: PDB REMARK 900 RELATED ID: 8PBJ RELATED DB: PDB REMARK 900 RELATED ID: 8PBK RELATED DB: PDB REMARK 900 RELATED ID: 8PBM RELATED DB: PDB REMARK 900 RELATED ID: 8PBN RELATED DB: PDB REMARK 900 RELATED ID: 8PBP RELATED DB: PDB REMARK 900 RELATED ID: 8PBQ RELATED DB: PDB DBREF 8PBT A 1460 1821 UNP P27708 PYR1_HUMAN 1460 1821 SEQADV 8PBT MET A 1482 UNP P27708 LYS 1482 ENGINEERED MUTATION SEQRES 1 A 362 LYS LEU VAL ARG LEU PRO GLY LEU ILE ASP VAL HIS VAL SEQRES 2 A 362 HIS LEU ARG GLU PRO GLY GLY THR HIS MET GLU ASP PHE SEQRES 3 A 362 ALA SER GLY THR ALA ALA ALA LEU ALA GLY GLY ILE THR SEQRES 4 A 362 MET VAL CYS ALA MET PRO ASN THR ARG PRO PRO ILE ILE SEQRES 5 A 362 ASP ALA PRO ALA LEU ALA LEU ALA GLN LYS LEU ALA GLU SEQRES 6 A 362 ALA GLY ALA ARG CYS ASP PHE ALA LEU PHE LEU GLY ALA SEQRES 7 A 362 SER SER GLU ASN ALA GLY THR LEU GLY THR VAL ALA GLY SEQRES 8 A 362 SER ALA ALA GLY LEU KCX LEU TYR LEU ASN GLU THR PHE SEQRES 9 A 362 SER GLU LEU ARG LEU ASP SER VAL VAL GLN TRP MET GLU SEQRES 10 A 362 HIS PHE GLU THR TRP PRO SER HIS LEU PRO ILE VAL ALA SEQRES 11 A 362 HIS ALA GLU GLN GLN THR VAL ALA ALA VAL LEU MET VAL SEQRES 12 A 362 ALA GLN LEU THR GLN ARG SER VAL HIS ILE CYS HIS VAL SEQRES 13 A 362 ALA ARG LYS GLU GLU ILE LEU LEU ILE LYS ALA ALA LYS SEQRES 14 A 362 ALA ARG GLY LEU PRO VAL THR CYS GLU VAL ALA PRO HIS SEQRES 15 A 362 HIS LEU PHE LEU SER HIS ASP ASP LEU GLU ARG LEU GLY SEQRES 16 A 362 PRO GLY LYS GLY GLU VAL ARG PRO GLU LEU GLY SER ARG SEQRES 17 A 362 GLN ASP VAL GLU ALA LEU TRP GLU ASN MET ALA VAL ILE SEQRES 18 A 362 ASP CYS PHE ALA SER ASP HIS ALA PRO HIS THR LEU GLU SEQRES 19 A 362 GLU LYS CYS GLY SER ARG PRO PRO PRO GLY PHE PRO GLY SEQRES 20 A 362 LEU GLU THR MET LEU PRO LEU LEU LEU THR ALA VAL SER SEQRES 21 A 362 GLU GLY ARG LEU SER LEU ASP ASP LEU LEU GLN ARG LEU SEQRES 22 A 362 HIS HIS ASN PRO ARG ARG ILE PHE HIS LEU PRO PRO GLN SEQRES 23 A 362 GLU ASP THR TYR VAL GLU VAL ASP LEU GLU HIS GLU TRP SEQRES 24 A 362 THR ILE PRO SER HIS MET PRO PHE SER LYS ALA HIS TRP SEQRES 25 A 362 THR PRO PHE GLU GLY GLN LYS VAL LYS GLY THR VAL ARG SEQRES 26 A 362 ARG VAL VAL LEU ARG GLY GLU VAL ALA TYR ILE ASP GLY SEQRES 27 A 362 GLN VAL LEU VAL PRO PRO GLY TYR GLY GLN ASP VAL ARG SEQRES 28 A 362 LYS TRP PRO GLN GLY ALA VAL PRO GLN LEU PRO MODRES 8PBT KCX A 1556 LYS MODIFIED RESIDUE HET KCX A1556 22 HET GOL A1901 13 HET DOR A1902 16 HET ZN A1903 1 HET ZN A1904 1 HET ZN A1905 1 HET ZN A1906 1 HET ZN A1907 1 HET ZN A1908 1 HET ZN A1909 1 HET FMT A1910 4 HET FMT A1911 4 HET FMT A1912 4 HET FMT A1913 4 HET FMT A1914 4 HET FMT A1915 4 HET FMT A1916 4 HET FMT A1917 4 HET FMT A1918 4 HET FMT A1919 5 HET FMT A1920 5 HET FMT A1921 5 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM GOL GLYCEROL HETNAM DOR (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID HETNAM ZN ZINC ION HETNAM FMT FORMIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN DOR DIHYDROOROTIC ACID FORMUL 1 KCX C7 H14 N2 O4 FORMUL 2 GOL C3 H8 O3 FORMUL 3 DOR C5 H6 N2 O4 FORMUL 4 ZN 7(ZN 2+) FORMUL 11 FMT 12(C H2 O2) FORMUL 23 HOH *330(H2 O) HELIX 1 AA1 ASP A 1484 GLY A 1495 1 12 HELIX 2 AA2 ASP A 1512 ALA A 1527 1 16 HELIX 3 AA3 VAL A 1548 ALA A 1552 5 5 HELIX 4 AA4 PHE A 1563 ARG A 1567 5 5 HELIX 5 AA5 SER A 1570 TRP A 1581 1 12 HELIX 6 AA6 GLN A 1593 THR A 1606 1 14 HELIX 7 AA7 ARG A 1617 ARG A 1630 1 14 HELIX 8 AA8 ALA A 1639 LEU A 1645 1 7 HELIX 9 AA9 SER A 1646 ASP A 1648 5 3 HELIX 10 AB1 ASP A 1649 GLY A 1658 1 10 HELIX 11 AB2 SER A 1666 ASN A 1676 1 11 HELIX 12 AB3 MET A 1677 ILE A 1680 5 4 HELIX 13 AB4 THR A 1691 CYS A 1696 1 6 HELIX 14 AB5 GLY A 1706 GLU A 1720 1 15 HELIX 15 AB6 SER A 1724 HIS A 1733 1 10 HELIX 16 AB7 HIS A 1733 HIS A 1741 1 9 HELIX 17 AB8 ASP A 1808 ALA A 1816 5 9 SHEET 1 AA1 5 VAL A1462 PRO A1465 0 SHEET 2 AA1 5 TYR A1749 THR A1759 -1 O VAL A1750 N LEU A1464 SHEET 3 AA1 5 LYS A1778 LEU A1788 -1 O ARG A1785 N GLU A1751 SHEET 4 AA1 5 GLU A1791 ILE A1795 -1 O ALA A1793 N VAL A1786 SHEET 5 AA1 5 GLN A1798 VAL A1799 -1 O GLN A1798 N ILE A1795 SHEET 1 AA2 3 LEU A1467 VAL A1472 0 SHEET 2 AA2 3 ILE A1497 ALA A1502 1 O THR A1498 N LEU A1467 SHEET 3 AA2 3 ASP A1530 LEU A1533 1 O ALA A1532 N ALA A1502 SHEET 1 AA3 6 LEU A1535 GLY A1536 0 SHEET 2 AA3 6 LEU A1555 TYR A1558 1 O KCX A1556 N LEU A1535 SHEET 3 AA3 6 ILE A1587 HIS A1590 1 O VAL A1588 N LEU A1555 SHEET 4 AA3 6 VAL A1610 ILE A1612 1 O HIS A1611 N ALA A1589 SHEET 5 AA3 6 VAL A1634 VAL A1638 1 O THR A1635 N ILE A1612 SHEET 6 AA3 6 CYS A1682 PHE A1683 1 O CYS A1682 N VAL A1638 SSBOND 1 CYS A 1696 CYS A 1696 1555 3454 2.59 LINK C LEU A1555 N KCX A1556 1555 1555 1.32 LINK C KCX A1556 N LEU A1557 1555 1555 1.33 LINK ND1 HIS A1471 ZN ZN A1905 1555 1555 2.10 LINK NE2 HIS A1471 ZN ZN A1907 1555 1555 2.02 LINK NE2 HIS A1473 ZN ZN A1907 1555 1555 2.00 LINK NE2 HIS A1481 ZN ZN A1903 1555 1555 1.92 LINK OQ1 KCX A1556 ZN ZN A1904 1555 1555 1.95 LINK OQ2 KCX A1556 ZN ZN A1907 1555 1555 2.25 LINK ND1 HIS A1590 ZN ZN A1904 1555 1555 2.08 LINK SG CYS A1613 ZN ZN A1905 1555 1555 2.52 LINK NE2 HIS A1614 ZN ZN A1904 1555 1555 2.05 LINK OE2 GLU A1637 ZN ZN A1905 1555 1555 2.24 LINK OD1 ASP A1686 ZN ZN A1907 1555 1555 2.12 LINK ND1 HIS A1690 ZN ZN A1903 1555 1555 2.04 LINK OE1 GLU A1694 ZN ZN A1903 1555 1555 1.97 LINK NE2 HIS A1734 ZN ZN A1906 1555 3554 2.07 LINK ND1 HIS A1741 ZN ZN A1906 1555 1555 2.03 LINK OD2 ASP A1753 ZN ZN A1908 1555 1555 1.89 LINK ND1 HIS A1756 ZN ZN A1908 1555 1555 2.66 LINK O GLN A1814 ZN ZN A1909 1555 1555 2.55 LINK O ALA A1816 ZN ZN A1909 1555 1555 2.20 LINK ZN ZN A1903 O1 FMT A1917 1555 1555 2.16 LINK ZN ZN A1904 O HOH A2104 1555 1555 1.97 LINK ZN ZN A1905 O HOH A2124 1555 1555 2.08 LINK ZN ZN A1906 O2 FMT A1914 1555 1555 2.03 LINK ZN ZN A1906 O1 FMT A1914 1555 1555 2.58 LINK ZN ZN A1906 O1 FMT A1915 1555 1555 1.95 LINK ZN ZN A1907 O HOH A2104 1555 1555 1.93 LINK ZN ZN A1908 O HOH A2247 1555 1555 2.36 LINK ZN ZN A1908 O HOH A2253 1555 1555 2.10 LINK ZN ZN A1909 O2 FMT A1915 1555 1555 2.21 LINK ZN ZN A1909 O HOH A2097 1555 1555 2.22 LINK ZN ZN A1909 O HOH A2172 1555 1555 2.25 CISPEP 1 GLU A 1476 PRO A 1477 0 3.64 CISPEP 2 ARG A 1507 PRO A 1508 0 1.07 CISPEP 3 ARG A 1661 PRO A 1662 0 -1.89 CRYST1 82.067 158.720 61.115 90.00 90.00 90.00 C 2 2 21 8 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 0.012185 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006300 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016363 0.00000