PDB Short entry for 3G3D HEADER LYASE 02-FEB-09 3G3D TITLE CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE TITLE 2 COVALENTLY MODIFIED BY 5-FLUORO-6-AZIDO-UMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: URIDINE 5'-MONOPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 190-480, OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPND 5 DOMAIN; COMPND 6 SYNONYM: UMP SYNTHASE; COMPND 7 EC: 4.1.1.23; COMPND 8 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: GI|13960142, OK/SW-CL.21, UMPS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS UMP SYNTHASE, C-TERMINAL DOMAIN, OROTIDINE 5'-MONOPHOSPHATE KEYWDS 2 DECARBOXYLASE, HUMAN, 5-FLUORO-6-AZIDO-UMP, DECARBOXYLASE, DISEASE KEYWDS 3 MUTATION, GLYCOSYLTRANSFERASE, LYASE, MULTIFUNCTIONAL ENZYME, KEYWDS 4 PHOSPHOPROTEIN, PYRIMIDINE BIOSYNTHESIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,H.L.TANG,A.BELLO,E.PODUCH,L.KOTRA,E.PAI REVDAT 4 06-SEP-23 3G3D 1 SEQADV LINK REVDAT 3 13-JUL-11 3G3D 1 VERSN REVDAT 2 31-MAR-09 3G3D 1 JRNL REVDAT 1 03-MAR-09 3G3D 0 JRNL AUTH A.M.BELLO,D.KONFORTE,E.PODUCH,C.FURLONGER,L.WEI,Y.LIU, JRNL AUTH 2 M.LEWIS,E.F.PAI,C.J.PAIGE,L.P.KOTRA JRNL TITL STRUCTURE-ACTIVITY RELATIONSHIPS OF JRNL TITL 2 OROTIDINE-5'-MONOPHOSPHATE DECARBOXYLASE INHIBITORS AS JRNL TITL 3 ANTICANCER AGENTS. JRNL REF J.MED.CHEM. V. 52 1648 2009 JRNL REFN ISSN 0022-2623 JRNL PMID 19260677 JRNL DOI 10.1021/JM801224T REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0066 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 54927 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2927 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2753 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 159 REMARK 3 BIN FREE R VALUE : 0.3780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3937 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 331 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.34000 REMARK 3 B22 (A**2) : -1.43000 REMARK 3 B33 (A**2) : 2.41000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.110 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.087 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.729 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4405 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5992 ; 1.538 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 579 ; 5.851 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 184 ;34.441 ;23.859 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 786 ;14.460 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;18.074 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 669 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3333 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2754 ; 0.744 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4446 ; 1.360 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1651 ; 2.325 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1546 ; 3.769 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3G3D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051371. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MONOCHROMATOR SI(111) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58024 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : 0.07400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.2000 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) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.49300 REMARK 200 R SYM FOR SHELL (I) : 0.49300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.765 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2P1F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PH 8.4, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 30.92500 REMARK 290 SMTRY3 2 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: 5990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 MET A -20 REMARK 465 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 LEU A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 REMARK 465 ARG A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 ASP A 1 REMARK 465 ALA A 2 REMARK 465 GLU A 3 REMARK 465 THR A 4 REMARK 465 VAL A 5 REMARK 465 GLY A 6 REMARK 465 ARG A 7 REMARK 465 VAL A 8 REMARK 465 LYS A 9 REMARK 465 ARG A 10 REMARK 465 PHE A 11 REMARK 465 ILE A 12 REMARK 465 GLN A 13 REMARK 465 GLU A 14 REMARK 465 ASN A 15 REMARK 465 VAL A 16 REMARK 465 PHE A 17 REMARK 465 VAL A 18 REMARK 465 ALA A 19 REMARK 465 ALA A 20 REMARK 465 ASN A 21 REMARK 465 HIS A 22 REMARK 465 ASN A 23 REMARK 465 GLY A 24 REMARK 465 SER A 25 REMARK 465 PRO A 26 REMARK 465 LEU A 27 REMARK 465 SER A 28 REMARK 465 ILE A 29 REMARK 465 LYS A 30 REMARK 465 GLU A 31 REMARK 465 ALA A 32 REMARK 465 PRO A 33 REMARK 465 LYS A 34 REMARK 465 VAL A 291 REMARK 465 MET B -20 REMARK 465 GLY B -19 REMARK 465 SER B -18 REMARK 465 SER B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 SER B -10 REMARK 465 SER B -9 REMARK 465 GLY B -8 REMARK 465 LEU B -7 REMARK 465 VAL B -6 REMARK 465 PRO B -5 REMARK 465 ARG B -4 REMARK 465 GLY B -3 REMARK 465 SER B -2 REMARK 465 HIS B -1 REMARK 465 MET B 0 REMARK 465 ASP B 1 REMARK 465 ALA B 2 REMARK 465 GLU B 3 REMARK 465 THR B 4 REMARK 465 VAL B 5 REMARK 465 GLY B 6 REMARK 465 ARG B 7 REMARK 465 VAL B 8 REMARK 465 LYS B 9 REMARK 465 ARG B 10 REMARK 465 PHE B 11 REMARK 465 ILE B 12 REMARK 465 GLN B 13 REMARK 465 GLU B 14 REMARK 465 ASN B 15 REMARK 465 VAL B 16 REMARK 465 PHE B 17 REMARK 465 VAL B 18 REMARK 465 ALA B 19 REMARK 465 ALA B 20 REMARK 465 ASN B 21 REMARK 465 HIS B 22 REMARK 465 ASN B 23 REMARK 465 GLY B 24 REMARK 465 SER B 25 REMARK 465 PRO B 26 REMARK 465 LEU B 27 REMARK 465 SER B 28 REMARK 465 ILE B 29 REMARK 465 LYS B 30 REMARK 465 GLU B 31 REMARK 465 VAL B 291 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 124 C LYS A 125 N 0.178 REMARK 500 LYS A 125 C PHE A 126 N 0.193 REMARK 500 LYS B 125 C PHE B 126 N 0.143 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS B 125 O - C - N ANGL. DEV. = -13.8 DEGREES 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 GLU A 117 72.27 64.06 REMARK 500 ASP A 123 58.65 -90.70 REMARK 500 ALA A 127 56.22 -159.23 REMARK 500 GLU B 117 72.27 68.09 REMARK 500 ALA B 127 54.21 -157.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5FU A3000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5FU B3000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B2000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3G3M RELATED DB: PDB DBREF 3G3D A 1 291 UNP P11172 PYR5_HUMAN 190 480 DBREF 3G3D B 1 291 UNP P11172 PYR5_HUMAN 190 480 SEQADV 3G3D MET A -20 UNP P11172 EXPRESSION TAG SEQADV 3G3D GLY A -19 UNP P11172 EXPRESSION TAG SEQADV 3G3D SER A -18 UNP P11172 EXPRESSION TAG SEQADV 3G3D SER A -17 UNP P11172 EXPRESSION TAG SEQADV 3G3D HIS A -16 UNP P11172 EXPRESSION TAG SEQADV 3G3D HIS A -15 UNP P11172 EXPRESSION TAG SEQADV 3G3D HIS A -14 UNP P11172 EXPRESSION TAG SEQADV 3G3D HIS A -13 UNP P11172 EXPRESSION TAG SEQADV 3G3D HIS A -12 UNP P11172 EXPRESSION TAG SEQADV 3G3D HIS A -11 UNP P11172 EXPRESSION TAG SEQADV 3G3D SER A -10 UNP P11172 EXPRESSION TAG SEQADV 3G3D SER A -9 UNP P11172 EXPRESSION TAG SEQADV 3G3D GLY A -8 UNP P11172 EXPRESSION TAG SEQADV 3G3D LEU A -7 UNP P11172 EXPRESSION TAG SEQADV 3G3D VAL A -6 UNP P11172 EXPRESSION TAG SEQADV 3G3D PRO A -5 UNP P11172 EXPRESSION TAG SEQADV 3G3D ARG A -4 UNP P11172 EXPRESSION TAG SEQADV 3G3D GLY A -3 UNP P11172 EXPRESSION TAG SEQADV 3G3D SER A -2 UNP P11172 EXPRESSION TAG SEQADV 3G3D HIS A -1 UNP P11172 EXPRESSION TAG SEQADV 3G3D MET A 0 UNP P11172 EXPRESSION TAG SEQADV 3G3D MET B -20 UNP P11172 EXPRESSION TAG SEQADV 3G3D GLY B -19 UNP P11172 EXPRESSION TAG SEQADV 3G3D SER B -18 UNP P11172 EXPRESSION TAG SEQADV 3G3D SER B -17 UNP P11172 EXPRESSION TAG SEQADV 3G3D HIS B -16 UNP P11172 EXPRESSION TAG SEQADV 3G3D HIS B -15 UNP P11172 EXPRESSION TAG SEQADV 3G3D HIS B -14 UNP P11172 EXPRESSION TAG SEQADV 3G3D HIS B -13 UNP P11172 EXPRESSION TAG SEQADV 3G3D HIS B -12 UNP P11172 EXPRESSION TAG SEQADV 3G3D HIS B -11 UNP P11172 EXPRESSION TAG SEQADV 3G3D SER B -10 UNP P11172 EXPRESSION TAG SEQADV 3G3D SER B -9 UNP P11172 EXPRESSION TAG SEQADV 3G3D GLY B -8 UNP P11172 EXPRESSION TAG SEQADV 3G3D LEU B -7 UNP P11172 EXPRESSION TAG SEQADV 3G3D VAL B -6 UNP P11172 EXPRESSION TAG SEQADV 3G3D PRO B -5 UNP P11172 EXPRESSION TAG SEQADV 3G3D ARG B -4 UNP P11172 EXPRESSION TAG SEQADV 3G3D GLY B -3 UNP P11172 EXPRESSION TAG SEQADV 3G3D SER B -2 UNP P11172 EXPRESSION TAG SEQADV 3G3D HIS B -1 UNP P11172 EXPRESSION TAG SEQADV 3G3D MET B 0 UNP P11172 EXPRESSION TAG SEQRES 1 A 312 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 312 LEU VAL PRO ARG GLY SER HIS MET ASP ALA GLU THR VAL SEQRES 3 A 312 GLY ARG VAL LYS ARG PHE ILE GLN GLU ASN VAL PHE VAL SEQRES 4 A 312 ALA ALA ASN HIS ASN GLY SER PRO LEU SER ILE LYS GLU SEQRES 5 A 312 ALA PRO LYS GLU LEU SER PHE GLY ALA ARG ALA GLU LEU SEQRES 6 A 312 PRO ARG ILE HIS PRO VAL ALA SER LYS LEU LEU ARG LEU SEQRES 7 A 312 MET GLN LYS LYS GLU THR ASN LEU CYS LEU SER ALA ASP SEQRES 8 A 312 VAL SER LEU ALA ARG GLU LEU LEU GLN LEU ALA ASP ALA SEQRES 9 A 312 LEU GLY PRO SER ILE CYS MET LEU LYS THR HIS VAL ASP SEQRES 10 A 312 ILE LEU ASN ASP PHE THR LEU ASP VAL MET LYS GLU LEU SEQRES 11 A 312 ILE THR LEU ALA LYS CYS HIS GLU PHE LEU ILE PHE GLU SEQRES 12 A 312 ASP ARG LYS PHE ALA ASP ILE GLY ASN THR VAL LYS LYS SEQRES 13 A 312 GLN TYR GLU GLY GLY ILE PHE LYS ILE ALA SER TRP ALA SEQRES 14 A 312 ASP LEU VAL ASN ALA HIS VAL VAL PRO GLY SER GLY VAL SEQRES 15 A 312 VAL LYS GLY LEU GLN GLU VAL GLY LEU PRO LEU HIS ARG SEQRES 16 A 312 GLY CYS LEU LEU ILE ALA GLU MET SER SER THR GLY SER SEQRES 17 A 312 LEU ALA THR GLY ASP TYR THR ARG ALA ALA VAL ARG MET SEQRES 18 A 312 ALA GLU GLU HIS SER GLU PHE VAL VAL GLY PHE ILE SER SEQRES 19 A 312 GLY SER ARG VAL SER MET LYS PRO GLU PHE LEU HIS LEU SEQRES 20 A 312 THR PRO GLY VAL GLN LEU GLU ALA GLY GLY ASP ASN LEU SEQRES 21 A 312 GLY GLN GLN TYR ASN SER PRO GLN GLU VAL ILE GLY LYS SEQRES 22 A 312 ARG GLY SER ASP ILE ILE ILE VAL GLY ARG GLY ILE ILE SEQRES 23 A 312 SER ALA ALA ASP ARG LEU GLU ALA ALA GLU MET TYR ARG SEQRES 24 A 312 LYS ALA ALA TRP GLU ALA TYR LEU SER ARG LEU GLY VAL SEQRES 1 B 312 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 312 LEU VAL PRO ARG GLY SER HIS MET ASP ALA GLU THR VAL SEQRES 3 B 312 GLY ARG VAL LYS ARG PHE ILE GLN GLU ASN VAL PHE VAL SEQRES 4 B 312 ALA ALA ASN HIS ASN GLY SER PRO LEU SER ILE LYS GLU SEQRES 5 B 312 ALA PRO LYS GLU LEU SER PHE GLY ALA ARG ALA GLU LEU SEQRES 6 B 312 PRO ARG ILE HIS PRO VAL ALA SER LYS LEU LEU ARG LEU SEQRES 7 B 312 MET GLN LYS LYS GLU THR ASN LEU CYS LEU SER ALA ASP SEQRES 8 B 312 VAL SER LEU ALA ARG GLU LEU LEU GLN LEU ALA ASP ALA SEQRES 9 B 312 LEU GLY PRO SER ILE CYS MET LEU LYS THR HIS VAL ASP SEQRES 10 B 312 ILE LEU ASN ASP PHE THR LEU ASP VAL MET LYS GLU LEU SEQRES 11 B 312 ILE THR LEU ALA LYS CYS HIS GLU PHE LEU ILE PHE GLU SEQRES 12 B 312 ASP ARG LYS PHE ALA ASP ILE GLY ASN THR VAL LYS LYS SEQRES 13 B 312 GLN TYR GLU GLY GLY ILE PHE LYS ILE ALA SER TRP ALA SEQRES 14 B 312 ASP LEU VAL ASN ALA HIS VAL VAL PRO GLY SER GLY VAL SEQRES 15 B 312 VAL LYS GLY LEU GLN GLU VAL GLY LEU PRO LEU HIS ARG SEQRES 16 B 312 GLY CYS LEU LEU ILE ALA GLU MET SER SER THR GLY SER SEQRES 17 B 312 LEU ALA THR GLY ASP TYR THR ARG ALA ALA VAL ARG MET SEQRES 18 B 312 ALA GLU GLU HIS SER GLU PHE VAL VAL GLY PHE ILE SER SEQRES 19 B 312 GLY SER ARG VAL SER MET LYS PRO GLU PHE LEU HIS LEU SEQRES 20 B 312 THR PRO GLY VAL GLN LEU GLU ALA GLY GLY ASP ASN LEU SEQRES 21 B 312 GLY GLN GLN TYR ASN SER PRO GLN GLU VAL ILE GLY LYS SEQRES 22 B 312 ARG GLY SER ASP ILE ILE ILE VAL GLY ARG GLY ILE ILE SEQRES 23 B 312 SER ALA ALA ASP ARG LEU GLU ALA ALA GLU MET TYR ARG SEQRES 24 B 312 LYS ALA ALA TRP GLU ALA TYR LEU SER ARG LEU GLY VAL HET 5FU A3000 22 HET GOL A1000 6 HET 5FU B3000 22 HET GOL B1001 6 HET GOL B1002 6 HET SO4 B2000 5 HETNAM 5FU 5-FLUORO-URIDINE-5'-MONOPHOSPHATE HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 5FU 2(C9 H12 F N2 O9 P) FORMUL 4 GOL 3(C3 H8 O3) FORMUL 8 SO4 O4 S 2- FORMUL 9 HOH *331(H2 O) HELIX 1 1 SER A 37 ALA A 42 1 6 HELIX 2 2 HIS A 48 GLU A 62 1 15 HELIX 3 3 LEU A 73 GLY A 85 1 13 HELIX 4 4 PRO A 86 ILE A 88 5 3 HELIX 5 5 HIS A 94 LEU A 98 5 5 HELIX 6 6 THR A 102 GLU A 117 1 16 HELIX 7 7 ILE A 129 GLY A 139 1 11 HELIX 8 8 LYS A 143 ALA A 148 1 6 HELIX 9 9 SER A 159 LEU A 170 1 12 HELIX 10 10 THR A 190 HIS A 204 1 15 HELIX 11 11 SER A 245 LYS A 252 1 8 HELIX 12 12 GLY A 261 SER A 266 1 6 HELIX 13 13 ASP A 269 GLY A 290 1 22 HELIX 14 14 SER B 37 ALA B 42 1 6 HELIX 15 15 HIS B 48 GLU B 62 1 15 HELIX 16 16 LEU B 73 GLY B 85 1 13 HELIX 17 17 PRO B 86 ILE B 88 5 3 HELIX 18 18 HIS B 94 LEU B 98 5 5 HELIX 19 19 THR B 102 GLU B 117 1 16 HELIX 20 20 ILE B 129 GLY B 139 1 11 HELIX 21 21 LYS B 143 TRP B 147 5 5 HELIX 22 22 SER B 159 LEU B 170 1 12 HELIX 23 23 THR B 190 HIS B 204 1 15 HELIX 24 24 SER B 245 GLY B 251 1 7 HELIX 25 25 GLY B 261 SER B 266 1 6 HELIX 26 26 ASP B 269 GLY B 290 1 22 SHEET 1 A 9 LEU A 65 SER A 68 0 SHEET 2 A 9 MET A 90 THR A 93 1 O LYS A 92 N LEU A 67 SHEET 3 A 9 LEU A 119 PHE A 126 1 O ASP A 123 N THR A 93 SHEET 4 A 9 LEU A 150 HIS A 154 1 O HIS A 154 N PHE A 126 SHEET 5 A 9 GLY A 175 ILE A 179 1 O ILE A 179 N ALA A 153 SHEET 6 A 9 VAL A 208 ILE A 212 1 O VAL A 209 N CYS A 176 SHEET 7 A 9 LEU A 224 THR A 227 1 O LEU A 224 N PHE A 211 SHEET 8 A 9 ILE A 257 VAL A 260 1 O ILE A 257 N THR A 227 SHEET 9 A 9 LEU A 65 SER A 68 1 N CYS A 66 O ILE A 258 SHEET 1 B 2 GLY A 235 GLY A 236 0 SHEET 2 B 2 GLN A 242 TYR A 243 -1 O TYR A 243 N GLY A 235 SHEET 1 C 9 LEU B 65 SER B 68 0 SHEET 2 C 9 MET B 90 THR B 93 1 O LYS B 92 N LEU B 67 SHEET 3 C 9 LEU B 119 PHE B 126 1 O ASP B 123 N THR B 93 SHEET 4 C 9 LEU B 150 HIS B 154 1 O HIS B 154 N PHE B 126 SHEET 5 C 9 GLY B 175 ILE B 179 1 O ILE B 179 N ALA B 153 SHEET 6 C 9 VAL B 208 ILE B 212 1 O VAL B 209 N CYS B 176 SHEET 7 C 9 LEU B 224 THR B 227 1 O LEU B 226 N PHE B 211 SHEET 8 C 9 ILE B 257 VAL B 260 1 O ILE B 257 N THR B 227 SHEET 9 C 9 LEU B 65 SER B 68 1 N CYS B 66 O ILE B 258 SHEET 1 D 2 GLY B 235 GLY B 236 0 SHEET 2 D 2 GLN B 242 TYR B 243 -1 O TYR B 243 N GLY B 235 LINK NZ LYS A 125 C6 5FU A3000 1555 1555 1.38 LINK NZ LYS B 125 C6 5FU B3000 1555 1555 1.37 CISPEP 1 LEU B 289 GLY B 290 0 -1.74 SITE 1 AC1 20 SER A 68 ASP A 70 LYS A 92 HIS A 94 SITE 2 AC1 20 ASP A 123 LYS A 125 MET A 182 SER A 183 SITE 3 AC1 20 PRO A 228 GLN A 241 TYR A 243 GLY A 261 SITE 4 AC1 20 ARG A 262 HOH A 295 HOH A 297 HOH A 298 SITE 5 AC1 20 HOH A 330 ASP B 128 ILE B 129 THR B 132 SITE 1 AC2 19 ASP A 128 ILE A 129 THR A 132 SER B 68 SITE 2 AC2 19 ASP B 70 LYS B 92 HIS B 94 ASP B 123 SITE 3 AC2 19 LYS B 125 MET B 182 SER B 183 PRO B 228 SITE 4 AC2 19 GLN B 241 TYR B 243 GLY B 261 ARG B 262 SITE 5 AC2 19 HOH B 300 HOH B 338 HOH B 345 SITE 1 AC3 7 LYS A 53 ALA A 113 LYS A 114 PHE A 118 SITE 2 AC3 7 LEU A 119 ASP A 149 HOH A 390 SITE 1 AC4 2 LEU B 73 ARG B 75 SITE 1 AC5 5 ASP B 269 GLU B 272 MET B 276 HOH B 348 SITE 2 AC5 5 HOH B 425 SITE 1 AC6 4 GLY B 39 ALA B 40 GLU B 43 HOH B 359 CRYST1 69.682 61.850 70.320 90.00 112.73 90.00 P 1 21 1 4 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 0.014351 0.000000 0.006010 0.00000 SCALE2 0.000000 0.016168 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015418 0.00000