HEADER TRANSFERASE 13-FEB-08 2ZI7 TITLE C4S DCK VARIANT OF DCK IN COMPLEX WITH D-DG+UDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYCYTIDINE KINASE; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: DCK; COMPND 5 EC: 2.7.1.74; COMPND 6 ENGINEERED: YES; COMPND 7 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: DCK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET14B KEYWDS DCK, PURINE, DEOXYGUANOSINE, DEOXYCYTIDINE KINASE, NUCLEOSIDE, KEYWDS 2 ENANTIOMER, D-DG, DG, ATP-BINDING, NUCLEOTIDE-BINDING, NUCLEUS, KEYWDS 3 PHOSPHOPROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR E.SABINI,A.LAVIE REVDAT 6 25-DEC-24 2ZI7 1 REMARK LINK REVDAT 5 01-NOV-23 2ZI7 1 REMARK REVDAT 4 10-NOV-21 2ZI7 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2ZI7 1 VERSN REVDAT 2 05-AUG-08 2ZI7 1 JRNL REVDAT 1 08-JUL-08 2ZI7 0 JRNL AUTH E.SABINI,S.HAZRA,M.KONRAD,A.LAVIE JRNL TITL ELUCIDATION OF DIFFERENT BINDING MODES OF PURINE NUCLEOSIDES JRNL TITL 2 TO HUMAN DEOXYCYTIDINE KINASE JRNL REF J.MED.CHEM. V. 51 4219 2008 JRNL REFN ISSN 0022-2623 JRNL PMID 18570408 JRNL DOI 10.1021/JM800134T REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 32619 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3607 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) : 1.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2127 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.2810 REMARK 3 BIN FREE R VALUE SET COUNT : 239 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3525 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.93000 REMARK 3 B22 (A**2) : 1.99000 REMARK 3 B33 (A**2) : -1.06000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.194 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.135 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.788 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3704 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5034 ; 1.635 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 419 ; 6.031 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 184 ;40.649 ;24.457 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 630 ;18.126 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;22.009 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 542 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2783 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1665 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2486 ; 0.318 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 175 ; 0.179 ; 0.200 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): 42 ; 0.186 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.131 ; 0.200 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): 2178 ; 1.055 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3429 ; 1.762 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1812 ; 2.559 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1605 ; 3.739 ; 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 : 1.40 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 2ZI7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000028003. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-06 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 : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36226 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.45800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 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 1P5Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M SODIUM CITRATE, 100MM HEPES, REMARK 280 PH7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 21.90000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.20000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.20000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.90000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.75000 REMARK 290 SMTRY3 4 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: 5040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 B -18 REMARK 465 GLY B -17 REMARK 465 SER B -16 REMARK 465 SER B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 HIS B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 THR B 3 REMARK 465 PRO B 4 REMARK 465 PRO B 5 REMARK 465 LYS B 6 REMARK 465 ARG B 7 REMARK 465 SER B 8 REMARK 465 SER B 9 REMARK 465 PRO B 10 REMARK 465 SER B 11 REMARK 465 PHE B 12 REMARK 465 SER B 13 REMARK 465 ALA B 14 REMARK 465 SER B 15 REMARK 465 SER B 16 REMARK 465 GLU B 17 REMARK 465 GLY B 18 REMARK 465 THR B 19 REMARK 465 ARG B 20 REMARK 465 GLN B 62 REMARK 465 SER B 63 REMARK 465 THR B 64 REMARK 465 GLN B 65 REMARK 465 ASP B 66 REMARK 465 GLU B 67 REMARK 465 PHE B 68 REMARK 465 GLU B 69 REMARK 465 GLU B 70 REMARK 465 LEU B 71 REMARK 465 THR B 72 REMARK 465 MET B 73 REMARK 465 SER B 74 REMARK 465 GLN B 75 REMARK 465 LYS B 76 REMARK 465 GLY B 114 REMARK 465 LYS B 115 REMARK 465 LEU B 116 REMARK 465 LYS B 117 REMARK 465 ASP B 118 REMARK 465 ALA B 119 REMARK 465 GLU B 120 REMARK 465 LEU B 221 REMARK 465 LYS B 222 REMARK 465 THR B 223 REMARK 465 ASN B 224 REMARK 465 PHE B 225 REMARK 465 ASP B 226 REMARK 465 TYR B 227 REMARK 465 LEU B 228 REMARK 465 GLN B 229 REMARK 465 GLU B 230 REMARK 465 MET A -18 REMARK 465 GLY A -17 REMARK 465 SER A -16 REMARK 465 SER A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 THR A 3 REMARK 465 PRO A 4 REMARK 465 PRO A 5 REMARK 465 LYS A 6 REMARK 465 ARG A 7 REMARK 465 SER A 8 REMARK 465 SER A 9 REMARK 465 PRO A 10 REMARK 465 SER A 11 REMARK 465 PHE A 12 REMARK 465 SER A 13 REMARK 465 ALA A 14 REMARK 465 SER A 15 REMARK 465 SER A 16 REMARK 465 GLU A 17 REMARK 465 GLY A 18 REMARK 465 THR A 19 REMARK 465 ARG A 20 REMARK 465 GLN A 65 REMARK 465 ASP A 66 REMARK 465 GLU A 67 REMARK 465 PHE A 68 REMARK 465 GLU A 69 REMARK 465 GLU A 70 REMARK 465 LEU A 71 REMARK 465 THR A 72 REMARK 465 MET A 73 REMARK 465 SER A 74 REMARK 465 GLN A 75 REMARK 465 LYS A 76 REMARK 465 ASN A 77 REMARK 465 LYS A 222 REMARK 465 THR A 223 REMARK 465 ASN A 224 REMARK 465 PHE A 225 REMARK 465 ASP A 226 REMARK 465 TYR A 227 REMARK 465 LEU A 228 REMARK 465 GLN A 229 REMARK 465 GLU A 230 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 GLU B 46 CG CD OE1 OE2 REMARK 470 LYS B 121 CG CD CE NZ REMARK 470 LYS A 121 CG CD CE NZ REMARK 470 GLN A 168 CG CD OE1 NE2 REMARK 470 ARG A 219 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 244 CG OD1 OD2 REMARK 470 LYS A 245 CG CD CE NZ 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 OE2 GLU B 53 O5' GNG B 503 2.15 REMARK 500 OE2 GLU A 53 O5' GNG A 502 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 GLU B 183 CG GLU B 183 CD 0.098 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 LYS B 88 70.09 -153.04 REMARK 500 ARG B 128 -175.82 64.64 REMARK 500 ILE B 136 -64.08 -99.14 REMARK 500 ASP B 241 130.48 -39.02 REMARK 500 LYS A 88 67.33 -153.58 REMARK 500 ARG A 128 -177.83 59.55 REMARK 500 ILE A 136 -65.43 -107.62 REMARK 500 LYS A 245 61.84 -152.76 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 GNG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNG B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1P60 RELATED DB: PDB REMARK 900 WT DCK IN COMPLEX WITH D-DC+ADP REMARK 900 RELATED ID: 2NO1 RELATED DB: PDB REMARK 900 C4S DCK VARIANT OF DCK IN COMPLEX WITH D-DC+ADP REMARK 900 RELATED ID: 2NO7 RELATED DB: PDB REMARK 900 C4S DCK VARIANT OF DCK IN COMPLEX WITH L-DC+ADP REMARK 900 RELATED ID: 2ZI3 RELATED DB: PDB REMARK 900 C4S-E247A DCK VARIANT OF DCK IN COMPLEX WITH D-DA+ADP REMARK 900 RELATED ID: 2ZI4 RELATED DB: PDB REMARK 900 C4S DCK VARIANT OF DCK IN COMPLEX WITH L-DA+ADP REMARK 900 RELATED ID: 2ZI5 RELATED DB: PDB REMARK 900 C4S DCK VARIANT OF DCK IN COMPLEX WITH L-DA+UDP REMARK 900 RELATED ID: 2ZI6 RELATED DB: PDB REMARK 900 C4S DCK VARIANT OF DCK IN COMPLEX WITH D-DA+UDP REMARK 900 RELATED ID: 2ZI9 RELATED DB: PDB REMARK 900 C4S-E247A DCK VARIANT OF DCK IN COMPLEX WITH CLADRIBINE+ADP REMARK 900 RELATED ID: 2ZIA RELATED DB: PDB REMARK 900 C4S DCK VARIANT OF DCK IN COMPLEX WITH CLADRIBINE+UDP DBREF 2ZI7 B 1 260 UNP P27707 DCK_HUMAN 1 260 DBREF 2ZI7 A 1 260 UNP P27707 DCK_HUMAN 1 260 SEQADV 2ZI7 MET B -18 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 GLY B -17 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 SER B -16 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 SER B -15 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 HIS B -14 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 HIS B -13 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 HIS B -12 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 HIS B -11 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 HIS B -10 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 HIS B -9 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 SER B -8 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 GLY B -7 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 LEU B -6 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 VAL B -5 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 PRO B -4 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 ARG B -3 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 GLY B -2 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 SER B -1 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 HIS B 0 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 SER B 9 UNP P27707 CYS 9 ENGINEERED MUTATION SEQADV 2ZI7 SER B 45 UNP P27707 CYS 45 ENGINEERED MUTATION SEQADV 2ZI7 SER B 59 UNP P27707 CYS 59 ENGINEERED MUTATION SEQADV 2ZI7 SER B 146 UNP P27707 CYS 146 ENGINEERED MUTATION SEQADV 2ZI7 MET A -18 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 GLY A -17 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 SER A -16 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 SER A -15 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 HIS A -14 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 HIS A -13 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 HIS A -12 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 HIS A -11 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 HIS A -10 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 HIS A -9 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 SER A -8 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 GLY A -7 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 LEU A -6 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 VAL A -5 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 PRO A -4 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 ARG A -3 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 GLY A -2 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 SER A -1 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 HIS A 0 UNP P27707 EXPRESSION TAG SEQADV 2ZI7 SER A 9 UNP P27707 CYS 9 ENGINEERED MUTATION SEQADV 2ZI7 SER A 45 UNP P27707 CYS 45 ENGINEERED MUTATION SEQADV 2ZI7 SER A 59 UNP P27707 CYS 59 ENGINEERED MUTATION SEQADV 2ZI7 SER A 146 UNP P27707 CYS 146 ENGINEERED MUTATION SEQRES 1 B 279 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLY LEU SEQRES 2 B 279 VAL PRO ARG GLY SER HIS MET ALA THR PRO PRO LYS ARG SEQRES 3 B 279 SER SER PRO SER PHE SER ALA SER SER GLU GLY THR ARG SEQRES 4 B 279 ILE LYS LYS ILE SER ILE GLU GLY ASN ILE ALA ALA GLY SEQRES 5 B 279 LYS SER THR PHE VAL ASN ILE LEU LYS GLN LEU SER GLU SEQRES 6 B 279 ASP TRP GLU VAL VAL PRO GLU PRO VAL ALA ARG TRP SER SEQRES 7 B 279 ASN VAL GLN SER THR GLN ASP GLU PHE GLU GLU LEU THR SEQRES 8 B 279 MET SER GLN LYS ASN GLY GLY ASN VAL LEU GLN MET MET SEQRES 9 B 279 TYR GLU LYS PRO GLU ARG TRP SER PHE THR PHE GLN THR SEQRES 10 B 279 TYR ALA CYS LEU SER ARG ILE ARG ALA GLN LEU ALA SER SEQRES 11 B 279 LEU ASN GLY LYS LEU LYS ASP ALA GLU LYS PRO VAL LEU SEQRES 12 B 279 PHE PHE GLU ARG SER VAL TYR SER ASP ARG TYR ILE PHE SEQRES 13 B 279 ALA SER ASN LEU TYR GLU SER GLU SER MET ASN GLU THR SEQRES 14 B 279 GLU TRP THR ILE TYR GLN ASP TRP HIS ASP TRP MET ASN SEQRES 15 B 279 ASN GLN PHE GLY GLN SER LEU GLU LEU ASP GLY ILE ILE SEQRES 16 B 279 TYR LEU GLN ALA THR PRO GLU THR CYS LEU HIS ARG ILE SEQRES 17 B 279 TYR LEU ARG GLY ARG ASN GLU GLU GLN GLY ILE PRO LEU SEQRES 18 B 279 GLU TYR LEU GLU LYS LEU HIS TYR LYS HIS GLU SER TRP SEQRES 19 B 279 LEU LEU HIS ARG THR LEU LYS THR ASN PHE ASP TYR LEU SEQRES 20 B 279 GLN GLU VAL PRO ILE LEU THR LEU ASP VAL ASN GLU ASP SEQRES 21 B 279 PHE LYS ASP LYS TYR GLU SER LEU VAL GLU LYS VAL LYS SEQRES 22 B 279 GLU PHE LEU SER THR LEU SEQRES 1 A 279 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLY LEU SEQRES 2 A 279 VAL PRO ARG GLY SER HIS MET ALA THR PRO PRO LYS ARG SEQRES 3 A 279 SER SER PRO SER PHE SER ALA SER SER GLU GLY THR ARG SEQRES 4 A 279 ILE LYS LYS ILE SER ILE GLU GLY ASN ILE ALA ALA GLY SEQRES 5 A 279 LYS SER THR PHE VAL ASN ILE LEU LYS GLN LEU SER GLU SEQRES 6 A 279 ASP TRP GLU VAL VAL PRO GLU PRO VAL ALA ARG TRP SER SEQRES 7 A 279 ASN VAL GLN SER THR GLN ASP GLU PHE GLU GLU LEU THR SEQRES 8 A 279 MET SER GLN LYS ASN GLY GLY ASN VAL LEU GLN MET MET SEQRES 9 A 279 TYR GLU LYS PRO GLU ARG TRP SER PHE THR PHE GLN THR SEQRES 10 A 279 TYR ALA CYS LEU SER ARG ILE ARG ALA GLN LEU ALA SER SEQRES 11 A 279 LEU ASN GLY LYS LEU LYS ASP ALA GLU LYS PRO VAL LEU SEQRES 12 A 279 PHE PHE GLU ARG SER VAL TYR SER ASP ARG TYR ILE PHE SEQRES 13 A 279 ALA SER ASN LEU TYR GLU SER GLU SER MET ASN GLU THR SEQRES 14 A 279 GLU TRP THR ILE TYR GLN ASP TRP HIS ASP TRP MET ASN SEQRES 15 A 279 ASN GLN PHE GLY GLN SER LEU GLU LEU ASP GLY ILE ILE SEQRES 16 A 279 TYR LEU GLN ALA THR PRO GLU THR CYS LEU HIS ARG ILE SEQRES 17 A 279 TYR LEU ARG GLY ARG ASN GLU GLU GLN GLY ILE PRO LEU SEQRES 18 A 279 GLU TYR LEU GLU LYS LEU HIS TYR LYS HIS GLU SER TRP SEQRES 19 A 279 LEU LEU HIS ARG THR LEU LYS THR ASN PHE ASP TYR LEU SEQRES 20 A 279 GLN GLU VAL PRO ILE LEU THR LEU ASP VAL ASN GLU ASP SEQRES 21 A 279 PHE LYS ASP LYS TYR GLU SER LEU VAL GLU LYS VAL LYS SEQRES 22 A 279 GLU PHE LEU SER THR LEU HET GNG B 503 19 HET UDP B 301 25 HET GNG A 502 19 HET UDP A 301 25 HETNAM GNG 2'-DEOXY-GUANOSINE HETNAM UDP URIDINE-5'-DIPHOSPHATE FORMUL 3 GNG 2(C10 H13 N5 O4) FORMUL 4 UDP 2(C9 H14 N2 O12 P2) FORMUL 7 HOH *84(H2 O) HELIX 1 1 GLY B 33 SER B 45 1 13 HELIX 2 2 PRO B 54 SER B 59 1 6 HELIX 3 3 ASN B 80 LYS B 88 1 9 HELIX 4 4 LYS B 88 LEU B 112 1 25 HELIX 5 5 SER B 129 ILE B 136 1 8 HELIX 6 6 ILE B 136 SER B 144 1 9 HELIX 7 7 ASN B 148 GLY B 167 1 20 HELIX 8 8 THR B 181 GLY B 193 1 13 HELIX 9 9 PRO B 201 LEU B 217 1 17 HELIX 10 10 TYR B 246 LEU B 260 1 15 HELIX 11 11 GLY A 33 SER A 45 1 13 HELIX 12 12 PRO A 54 ASN A 60 1 7 HELIX 13 13 ASN A 80 LYS A 88 1 9 HELIX 14 14 LYS A 88 LYS A 115 1 28 HELIX 15 15 SER A 129 ILE A 136 1 8 HELIX 16 16 ILE A 136 SER A 144 1 9 HELIX 17 17 ASN A 148 GLU A 171 1 24 HELIX 18 18 THR A 181 GLY A 193 1 13 HELIX 19 19 ARG A 194 GLN A 198 5 5 HELIX 20 20 PRO A 201 LEU A 217 1 17 HELIX 21 21 TYR A 246 THR A 259 1 14 SHEET 1 A 5 TRP B 48 VAL B 51 0 SHEET 2 A 5 VAL B 123 GLU B 127 1 O PHE B 125 N VAL B 51 SHEET 3 A 5 LYS B 22 GLY B 28 1 N ILE B 24 O PHE B 126 SHEET 4 A 5 GLY B 174 GLN B 179 1 O ILE B 176 N SER B 25 SHEET 5 A 5 ILE B 233 ASP B 237 1 O LEU B 234 N TYR B 177 SHEET 1 B 5 TRP A 48 VAL A 51 0 SHEET 2 B 5 VAL A 123 GLU A 127 1 O GLU A 127 N VAL A 51 SHEET 3 B 5 LYS A 22 GLY A 28 1 N LYS A 22 O LEU A 124 SHEET 4 B 5 GLY A 174 GLN A 179 1 O LEU A 178 N GLU A 27 SHEET 5 B 5 ILE A 233 ASP A 237 1 O LEU A 234 N TYR A 177 SITE 1 AC1 15 ILE A 30 GLU A 53 TRP A 58 LEU A 82 SITE 2 AC1 15 MET A 85 TYR A 86 PHE A 96 GLN A 97 SITE 3 AC1 15 ARG A 104 ARG A 128 ASP A 133 PHE A 137 SITE 4 AC1 15 LEU A 141 ARG A 194 GLU A 197 SITE 1 AC2 13 ILE B 30 GLU B 53 TRP B 58 LEU B 82 SITE 2 AC2 13 MET B 85 TYR B 86 PHE B 96 GLN B 97 SITE 3 AC2 13 ARG B 104 ARG B 128 ASP B 133 PHE B 137 SITE 4 AC2 13 GLU B 197 SITE 1 AC3 14 ALA A 31 ALA A 32 GLY A 33 LYS A 34 SITE 2 AC3 14 SER A 35 THR A 36 GLU A 127 ARG A 188 SITE 3 AC3 14 LEU A 191 ARG A 192 ASP A 241 PHE A 242 SITE 4 AC3 14 LYS A 243 GLU B 206 SITE 1 AC4 14 GLU A 206 ALA B 31 ALA B 32 GLY B 33 SITE 2 AC4 14 LYS B 34 SER B 35 THR B 36 GLU B 127 SITE 3 AC4 14 ARG B 188 LEU B 191 ARG B 192 ASP B 241 SITE 4 AC4 14 PHE B 242 LYS B 243 CRYST1 43.800 107.500 110.400 90.00 90.00 90.00 P 21 21 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 0.022831 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009302 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009058 0.00000