HEADER HYDROLASE 09-JUN-23 8PBQ TITLE MUTANT R1810Q OF THE DIHYDROOROTASE DOMAIN OF HUMAN CAD PROTEIN BOUND TITLE 2 TO THE SUBSTRATES 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: HEK293 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-R1810Q 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 8PBQ 1 JRNL REVDAT 2 15-NOV-23 8PBQ 1 REMARK REVDAT 1 01-NOV-23 8PBQ 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. 1.54 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 59780 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 2885 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 10.0000 - 4.2400 1.00 2895 151 0.1684 0.1893 REMARK 3 2 4.2400 - 3.3700 1.00 2759 152 0.1346 0.1521 REMARK 3 3 3.3700 - 2.9400 1.00 2729 150 0.1549 0.1581 REMARK 3 4 2.9400 - 2.6700 1.00 2756 126 0.1537 0.1971 REMARK 3 5 2.6700 - 2.4800 1.00 2723 119 0.1374 0.1597 REMARK 3 6 2.4800 - 2.3400 1.00 2724 129 0.1256 0.1632 REMARK 3 7 2.3400 - 2.2200 1.00 2715 139 0.1204 0.1754 REMARK 3 8 2.2200 - 2.1200 1.00 2679 145 0.1147 0.1411 REMARK 3 9 2.1200 - 2.0400 1.00 2695 138 0.1137 0.1464 REMARK 3 10 2.0400 - 1.9700 1.00 2670 146 0.1237 0.1831 REMARK 3 11 1.9700 - 1.9100 1.00 2701 143 0.1295 0.1734 REMARK 3 12 1.9100 - 1.8500 1.00 2701 135 0.1350 0.1772 REMARK 3 13 1.8500 - 1.8000 1.00 2692 122 0.1380 0.1807 REMARK 3 14 1.8000 - 1.7600 1.00 2718 136 0.1378 0.1742 REMARK 3 15 1.7600 - 1.7200 1.00 2644 143 0.1441 0.1733 REMARK 3 16 1.7200 - 1.6800 1.00 2677 146 0.1548 0.1937 REMARK 3 17 1.6800 - 1.6500 1.00 2688 132 0.1733 0.2284 REMARK 3 18 1.6500 - 1.6200 1.00 2673 125 0.1945 0.2550 REMARK 3 19 1.6200 - 1.5900 1.00 2686 134 0.2274 0.2663 REMARK 3 20 1.5900 - 1.5600 1.00 2681 136 0.2400 0.2727 REMARK 3 21 1.5600 - 1.5400 1.00 2689 138 0.2498 0.2750 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.151 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.904 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.61 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 2879 REMARK 3 ANGLE : 1.134 3963 REMARK 3 CHIRALITY : 0.061 456 REMARK 3 PLANARITY : 0.010 523 REMARK 3 DIHEDRAL : 7.682 415 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 8PBQ 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_1292130770. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.97918 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 393684 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 48.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 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 : 2.350 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 (%): 52.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES PH 7.5, 3.2M SODIUM REMARK 280 FORMATE, 2 MM CARBAMOYL ASPARTATE, 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 30.56200 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 30.56200 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 41.14700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 79.40500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.14700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 79.40500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.56200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.14700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 79.40500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 30.56200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.14700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 79.40500 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: 3460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -389.0 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 -30.56200 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 ARG A1567 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1651 CG CD OE1 OE2 REMARK 470 ARG A1667 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1675 CG CD OE1 OE2 REMARK 470 ARG A1699 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1778 CG CD CE NZ REMARK 470 ARG A1785 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1811 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 ARG A1475 -7.68 68.32 REMARK 500 GLU A1483 153.34 173.38 REMARK 500 ASN A1505 45.67 -87.00 REMARK 500 THR A1562 -167.62 -165.70 REMARK 500 GLN A1593 -126.06 51.06 REMARK 500 HIS A1614 76.37 19.30 REMARK 500 HIS A1733 -66.39 -149.03 REMARK 500 ASP A1796 60.55 36.30 REMARK 500 REMARK 500 REMARK: NULL 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 A1904 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1471 NE2 REMARK 620 2 HIS A1473 NE2 115.3 REMARK 620 3 KCX A1556 OQ1 89.7 92.0 REMARK 620 4 ASP A1686 OD1 85.9 92.8 174.6 REMARK 620 5 NCD A1901 O4 124.9 119.7 85.3 94.5 REMARK 620 N 1 2 3 4 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 114.5 REMARK 620 3 GLU A1637 OE2 82.8 114.1 REMARK 620 4 HOH A2113 O 122.9 109.8 110.0 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 GLU A1524 O REMARK 620 2 GLY A1804 O 91.4 REMARK 620 3 GLY A1806 O 109.9 96.3 REMARK 620 4 HOH A2182 O 76.6 83.8 173.4 REMARK 620 5 HOH A2205 O 109.5 151.0 95.1 81.8 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 KCX A1556 OQ2 REMARK 620 2 HIS A1590 ND1 107.3 REMARK 620 3 HIS A1614 NE2 108.8 97.5 REMARK 620 4 NCD A1901 O4 96.1 144.2 100.1 REMARK 620 5 NCD A1901 O5 116.3 85.6 131.6 59.5 REMARK 620 N 1 2 3 4 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 A1734 NE2 REMARK 620 2 HOH A2207 O 107.6 REMARK 620 3 HOH A2213 O 125.1 99.8 REMARK 620 N 1 2 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: 8PBT 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: 8PBL 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 DBREF 8PBQ A 1460 1813 UNP P27708 PYR1_HUMAN 1460 1813 SEQADV 8PBQ GLN A 1810 UNP P27708 ARG 1810 ENGINEERED MUTATION SEQRES 1 A 354 LYS LEU VAL ARG LEU PRO GLY LEU ILE ASP VAL HIS VAL SEQRES 2 A 354 HIS LEU ARG GLU PRO GLY GLY THR HIS LYS GLU ASP PHE SEQRES 3 A 354 ALA SER GLY THR ALA ALA ALA LEU ALA GLY GLY ILE THR SEQRES 4 A 354 MET VAL CYS ALA MET PRO ASN THR ARG PRO PRO ILE ILE SEQRES 5 A 354 ASP ALA PRO ALA LEU ALA LEU ALA GLN LYS LEU ALA GLU SEQRES 6 A 354 ALA GLY ALA ARG CYS ASP PHE ALA LEU PHE LEU GLY ALA SEQRES 7 A 354 SER SER GLU ASN ALA GLY THR LEU GLY THR VAL ALA GLY SEQRES 8 A 354 SER ALA ALA GLY LEU KCX LEU TYR LEU ASN GLU THR PHE SEQRES 9 A 354 SER GLU LEU ARG LEU ASP SER VAL VAL GLN TRP MET GLU SEQRES 10 A 354 HIS PHE GLU THR TRP PRO SER HIS LEU PRO ILE VAL ALA SEQRES 11 A 354 HIS ALA GLU GLN GLN THR VAL ALA ALA VAL LEU MET VAL SEQRES 12 A 354 ALA GLN LEU THR GLN ARG SER VAL HIS ILE CYS HIS VAL SEQRES 13 A 354 ALA ARG LYS GLU GLU ILE LEU LEU ILE LYS ALA ALA LYS SEQRES 14 A 354 ALA ARG GLY LEU PRO VAL THR CYS GLU VAL ALA PRO HIS SEQRES 15 A 354 HIS LEU PHE LEU SER HIS ASP ASP LEU GLU ARG LEU GLY SEQRES 16 A 354 PRO GLY LYS GLY GLU VAL ARG PRO GLU LEU GLY SER ARG SEQRES 17 A 354 GLN ASP VAL GLU ALA LEU TRP GLU ASN MET ALA VAL ILE SEQRES 18 A 354 ASP CYS PHE ALA SER ASP HIS ALA PRO HIS THR LEU GLU SEQRES 19 A 354 GLU LYS CYS GLY SER ARG PRO PRO PRO GLY PHE PRO GLY SEQRES 20 A 354 LEU GLU THR MET LEU PRO LEU LEU LEU THR ALA VAL SER SEQRES 21 A 354 GLU GLY ARG LEU SER LEU ASP ASP LEU LEU GLN ARG LEU SEQRES 22 A 354 HIS HIS ASN PRO ARG ARG ILE PHE HIS LEU PRO PRO GLN SEQRES 23 A 354 GLU ASP THR TYR VAL GLU VAL ASP LEU GLU HIS GLU TRP SEQRES 24 A 354 THR ILE PRO SER HIS MET PRO PHE SER LYS ALA HIS TRP SEQRES 25 A 354 THR PRO PHE GLU GLY GLN LYS VAL LYS GLY THR VAL ARG SEQRES 26 A 354 ARG VAL VAL LEU ARG GLY GLU VAL ALA TYR ILE ASP GLY SEQRES 27 A 354 GLN VAL LEU VAL PRO PRO GLY TYR GLY GLN ASP VAL GLN SEQRES 28 A 354 LYS TRP PRO MODRES 8PBQ KCX A 1556 LYS MODIFIED RESIDUE HET KCX A1556 22 HET NCD A1901 18 HET FMT A1902 5 HET ZN A1903 1 HET ZN A1904 1 HET ZN A1905 1 HET ZN A1906 1 HET ZN A1907 1 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM NCD N-CARBAMOYL-L-ASPARTATE HETNAM FMT FORMIC ACID HETNAM ZN ZINC ION FORMUL 1 KCX C7 H14 N2 O4 FORMUL 2 NCD C5 H8 N2 O5 FORMUL 3 FMT C H2 O2 FORMUL 4 ZN 5(ZN 2+) FORMUL 9 HOH *242(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 SER A 1570 TRP A 1581 1 12 HELIX 5 AA5 GLN A 1593 THR A 1606 1 14 HELIX 6 AA6 ARG A 1617 ARG A 1630 1 14 HELIX 7 AA7 ALA A 1639 LEU A 1645 1 7 HELIX 8 AA8 SER A 1646 ASP A 1648 5 3 HELIX 9 AA9 ASP A 1649 GLY A 1658 1 10 HELIX 10 AB1 SER A 1666 ASN A 1676 1 11 HELIX 11 AB2 MET A 1677 ILE A 1680 5 4 HELIX 12 AB3 THR A 1691 CYS A 1696 1 6 HELIX 13 AB4 GLY A 1706 GLU A 1720 1 15 HELIX 14 AB5 SER A 1724 HIS A 1733 1 10 HELIX 15 AB6 HIS A 1733 HIS A 1741 1 9 HELIX 16 AB7 ASP A 1808 TRP A 1812 5 5 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 MET A1499 N ASP A1469 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 HIS A1590 N LEU A1557 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 2.15 LINK C LEU A1555 N KCX A1556 1555 1555 1.34 LINK C KCX A1556 N LEU A1557 1555 1555 1.34 LINK NE2 HIS A1471 ZN ZN A1904 1555 1555 2.05 LINK ND1 HIS A1471 ZN ZN A1905 1555 1555 2.10 LINK NE2 HIS A1473 ZN ZN A1904 1555 1555 2.07 LINK O GLU A1524 ZN ZN A1906 1555 1555 2.46 LINK OQ2 KCX A1556 ZN ZN A1903 1555 1555 1.91 LINK OQ1 KCX A1556 ZN ZN A1904 1555 1555 2.20 LINK ND1 HIS A1590 ZN ZN A1903 1555 1555 2.12 LINK SG CYS A1613 ZN ZN A1905 1555 1555 2.34 LINK NE2 HIS A1614 ZN ZN A1903 1555 1555 2.14 LINK OE2 GLU A1637 ZN ZN A1905 1555 1555 2.18 LINK OD1 ASP A1686 ZN ZN A1904 1555 1555 2.03 LINK NE2 HIS A1734 ZN ZN A1907 1555 1555 2.17 LINK O GLY A1804 ZN ZN A1906 1555 1555 2.37 LINK O GLY A1806 ZN ZN A1906 1555 1555 2.26 LINK O4 NCD A1901 ZN ZN A1903 1555 1555 2.34 LINK O5 NCD A1901 ZN ZN A1903 1555 1555 2.16 LINK O4 NCD A1901 ZN ZN A1904 1555 1555 2.01 LINK ZN ZN A1905 O HOH A2113 1555 1555 2.03 LINK ZN ZN A1906 O HOH A2182 1555 1555 2.39 LINK ZN ZN A1906 O HOH A2205 1555 1555 2.54 LINK ZN ZN A1907 O HOH A2207 1555 1555 2.28 LINK ZN ZN A1907 O HOH A2213 1555 1555 2.04 CISPEP 1 GLU A 1476 PRO A 1477 0 3.49 CISPEP 2 ARG A 1507 PRO A 1508 0 1.90 CISPEP 3 ARG A 1661 PRO A 1662 0 -13.91 CRYST1 82.294 158.810 61.124 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 0.012152 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006297 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016360 0.00000