HEADER TRANSFERASE 25-OCT-06 2NO9 TITLE THE STRUCTURE OF DEOXYCYTIDINE KINASE COMPLEXED WITH TROXACITABINE AND TITLE 2 ADP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYCYTIDINE KINASE; COMPND 3 CHAIN: A, B; 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_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET14B KEYWDS DCK, TROXACITABINE, HUMAN DEOXYCYTIDINE KINASE, L-DC, ENANTIOMER, KEYWDS 2 ANTICANCER, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR E.SABINI,A.LAVIE REVDAT 4 20-OCT-21 2NO9 1 SEQADV REVDAT 3 03-FEB-21 2NO9 1 JRNL REMARK REVDAT 2 24-FEB-09 2NO9 1 VERSN REVDAT 1 13-FEB-07 2NO9 0 JRNL AUTH E.SABINI,S.HAZRA,M.KONRAD,S.K.BURLEY,A.LAVIE JRNL TITL STRUCTURAL BASIS FOR ACTIVATION OF THE THERAPEUTIC JRNL TITL 2 L-NUCLEOSIDE ANALOGS 3TC AND TROXACITABINE BY HUMAN JRNL TITL 3 DEOXYCYTIDINE KINASE. JRNL REF NUCLEIC ACIDS RES. V. 35 186 2007 JRNL REFN ISSN 0305-1048 JRNL PMID 17158155 JRNL DOI 10.1093/NAR/GKL1038 REMARK 2 REMARK 2 RESOLUTION. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 27466 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3070 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2005 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2160 REMARK 3 BIN FREE R VALUE SET COUNT : 235 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3850 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 84 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.23000 REMARK 3 B22 (A**2) : -0.70000 REMARK 3 B33 (A**2) : 0.47000 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): 0.258 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.217 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.146 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.467 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4033 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5483 ; 1.718 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 466 ; 6.092 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 202 ;39.473 ;24.455 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 681 ;17.245 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;18.746 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 590 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3067 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1722 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2761 ; 0.314 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 219 ; 0.174 ; 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): 62 ; 0.291 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.251 ; 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): 2402 ; 1.077 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3770 ; 1.793 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1923 ; 2.608 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1713 ; 3.851 ; 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 2NO9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000040104. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-05 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 : ROSENBAUM-ROCK MONOCHROMATOR REMARK 200 HIGH-RESOLUTION DOUBLE-CRYSTAL REMARK 200 SI (111) SAGITTAL FOCUSING, REMARK 200 ROSENBAUM-ROCK VERTICAL REMARK 200 OPTICS : MIRRORS 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30536 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09900 REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.51100 REMARK 200 FOR SHELL : 4.400 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: 1P5Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR CONTAINING 0.95-1.5M REMARK 280 TRISODIUM CITRATE DIHYDRATE AND 100MM HEPES, PH 7.5., VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 77.67000 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 77.67000 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 26.42500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 67.23000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.42500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 67.23000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 77.67000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.42500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 67.23000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 77.67000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.42500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 67.23000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: 5000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 134.46000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 155.34000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 26.42500 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 -67.23000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 26.42500 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 201.69000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 155.34000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 134.46000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 155.34000 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER 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 HIS A -10 REMARK 465 SER 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 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER 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 HIS B -10 REMARK 465 SER 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 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 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 THR A 19 OG1 CG2 REMARK 470 GLN A 43 CG CD OE1 NE2 REMARK 470 GLU A 46 CG CD OE1 OE2 REMARK 470 LYS A 117 CG CD CE NZ REMARK 470 ASP A 118 CG OD1 OD2 REMARK 470 GLU A 120 CG CD OE1 OE2 REMARK 470 LYS A 121 CG CD CE NZ REMARK 470 SER A 146 OG REMARK 470 GLN A 168 CG CD OE1 NE2 REMARK 470 TYR A 190 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 229 CG CD OE1 NE2 REMARK 470 GLU A 251 CG CD OE1 OE2 REMARK 470 SER B 45 OG REMARK 470 SER B 59 OG REMARK 470 LYS B 117 CG CD CE NZ REMARK 470 ASP B 118 CG OD1 OD2 REMARK 470 LYS B 121 CG CD CE NZ REMARK 470 GLN B 168 CG CD OE1 NE2 REMARK 470 LYS B 222 CG CD CE NZ REMARK 470 LYS B 243 CG CD CE NZ REMARK 470 GLU B 247 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 310 O HOH A 337 2.15 REMARK 500 O SER A 45 O HOH A 345 2.17 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 PRO A 54 44.83 -75.32 REMARK 500 ARG A 128 174.45 64.05 REMARK 500 ILE A 136 -69.12 -107.64 REMARK 500 ASN A 224 2.14 -69.93 REMARK 500 PRO B 54 48.80 -77.44 REMARK 500 LYS B 115 143.57 172.91 REMARK 500 LEU B 116 -125.28 64.85 REMARK 500 LYS B 117 -28.81 50.92 REMARK 500 GLU B 120 -71.99 -50.66 REMARK 500 ARG B 128 -179.43 67.17 REMARK 500 ILE B 136 -68.15 -107.48 REMARK 500 GLN B 165 -88.40 -80.97 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 ADP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LTT A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LTT B 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1P5Z RELATED DB: PDB REMARK 900 WILD TYPE HUMAN DEOXYCYTIDINE KINASE IN COMPLEX WITH CYTARABINE AND REMARK 900 ADP-MG REMARK 900 RELATED ID: 1P60 RELATED DB: PDB REMARK 900 WILD TYPE HUMAN DEOXYCYTIDINE KINASE IN COMPLEX WITH DEOXYCYTIDINE REMARK 900 AND ADP REMARK 900 RELATED ID: 1P61 RELATED DB: PDB REMARK 900 WILD TYPE HUMAN DEOXYCYTIDINE KINASE IN COMPLEX WITH DEOXYCYTIDINE REMARK 900 AND ADP REMARK 900 RELATED ID: 1P62 RELATED DB: PDB REMARK 900 WILD TYPE HUMAN DEOXYCYTIDINE KINASE IN COMPLEX WITH GEMCITABINE REMARK 900 AND ADP-MG REMARK 900 RELATED ID: 2A2Z RELATED DB: PDB REMARK 900 INSERT-DELETION MUTANT OF HUMAN DEOXYCYTIDINE KINASE IN COMPLEX REMARK 900 WITH DEOXYCYTIDINE AND UDP REMARK 900 RELATED ID: 2A30 RELATED DB: PDB REMARK 900 INSERT-DELETION MUTANT OF HUMAN DEOXYCYTIDINE KINASE IN COMPLEX REMARK 900 WITH DEOXYCYTIDINE REMARK 900 RELATED ID: 2NO0 RELATED DB: PDB REMARK 900 RELATED ID: 2NO1 RELATED DB: PDB REMARK 900 RELATED ID: 1NO6 RELATED DB: PDB REMARK 900 RELATED ID: 2NO7 RELATED DB: PDB REMARK 900 RELATED ID: 2NOA RELATED DB: PDB DBREF 2NO9 A 1 260 UNP P27707 DCK_HUMAN 1 260 DBREF 2NO9 B 1 260 UNP P27707 DCK_HUMAN 1 260 SEQADV 2NO9 MET A -19 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 GLY A -18 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 SER A -17 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 SER A -16 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 HIS A -15 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 HIS A -14 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 HIS A -13 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 HIS A -12 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 HIS A -11 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 HIS A -10 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 SER A -9 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 SER A -8 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 GLY A -7 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 LEU A -6 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 VAL A -5 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 PRO A -4 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 ARG A -3 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 GLY A -2 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 SER A -1 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 HIS A 0 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 SER A 9 UNP P27707 CYS 9 ENGINEERED MUTATION SEQADV 2NO9 SER A 45 UNP P27707 CYS 45 ENGINEERED MUTATION SEQADV 2NO9 SER A 59 UNP P27707 CYS 59 ENGINEERED MUTATION SEQADV 2NO9 SER A 146 UNP P27707 CYS 146 ENGINEERED MUTATION SEQADV 2NO9 MET B -19 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 GLY B -18 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 SER B -17 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 SER B -16 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 HIS B -15 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 HIS B -14 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 HIS B -13 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 HIS B -12 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 HIS B -11 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 HIS B -10 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 SER B -9 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 SER B -8 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 GLY B -7 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 LEU B -6 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 VAL B -5 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 PRO B -4 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 ARG B -3 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 GLY B -2 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 SER B -1 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 HIS B 0 UNP P27707 CLONING ARTIFACT SEQADV 2NO9 SER B 9 UNP P27707 CYS 9 ENGINEERED MUTATION SEQADV 2NO9 SER B 45 UNP P27707 CYS 45 ENGINEERED MUTATION SEQADV 2NO9 SER B 59 UNP P27707 CYS 59 ENGINEERED MUTATION SEQADV 2NO9 SER B 146 UNP P27707 CYS 146 ENGINEERED MUTATION SEQRES 1 A 280 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 280 LEU VAL PRO ARG GLY SER HIS MET ALA THR PRO PRO LYS SEQRES 3 A 280 ARG SER SER PRO SER PHE SER ALA SER SER GLU GLY THR SEQRES 4 A 280 ARG ILE LYS LYS ILE SER ILE GLU GLY ASN ILE ALA ALA SEQRES 5 A 280 GLY LYS SER THR PHE VAL ASN ILE LEU LYS GLN LEU SER SEQRES 6 A 280 GLU ASP TRP GLU VAL VAL PRO GLU PRO VAL ALA ARG TRP SEQRES 7 A 280 SER ASN VAL GLN SER THR GLN ASP GLU PHE GLU GLU LEU SEQRES 8 A 280 THR MET SER GLN LYS ASN GLY GLY ASN VAL LEU GLN MET SEQRES 9 A 280 MET TYR GLU LYS PRO GLU ARG TRP SER PHE THR PHE GLN SEQRES 10 A 280 THR TYR ALA CYS LEU SER ARG ILE ARG ALA GLN LEU ALA SEQRES 11 A 280 SER LEU ASN GLY LYS LEU LYS ASP ALA GLU LYS PRO VAL SEQRES 12 A 280 LEU PHE PHE GLU ARG SER VAL TYR SER ASP ARG TYR ILE SEQRES 13 A 280 PHE ALA SER ASN LEU TYR GLU SER GLU SER MET ASN GLU SEQRES 14 A 280 THR GLU TRP THR ILE TYR GLN ASP TRP HIS ASP TRP MET SEQRES 15 A 280 ASN ASN GLN PHE GLY GLN SER LEU GLU LEU ASP GLY ILE SEQRES 16 A 280 ILE TYR LEU GLN ALA THR PRO GLU THR CYS LEU HIS ARG SEQRES 17 A 280 ILE TYR LEU ARG GLY ARG ASN GLU GLU GLN GLY ILE PRO SEQRES 18 A 280 LEU GLU TYR LEU GLU LYS LEU HIS TYR LYS HIS GLU SER SEQRES 19 A 280 TRP LEU LEU HIS ARG THR LEU LYS THR ASN PHE ASP TYR SEQRES 20 A 280 LEU GLN GLU VAL PRO ILE LEU THR LEU ASP VAL ASN GLU SEQRES 21 A 280 ASP PHE LYS ASP LYS TYR GLU SER LEU VAL GLU LYS VAL SEQRES 22 A 280 LYS GLU PHE LEU SER THR LEU SEQRES 1 B 280 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 280 LEU VAL PRO ARG GLY SER HIS MET ALA THR PRO PRO LYS SEQRES 3 B 280 ARG SER SER PRO SER PHE SER ALA SER SER GLU GLY THR SEQRES 4 B 280 ARG ILE LYS LYS ILE SER ILE GLU GLY ASN ILE ALA ALA SEQRES 5 B 280 GLY LYS SER THR PHE VAL ASN ILE LEU LYS GLN LEU SER SEQRES 6 B 280 GLU ASP TRP GLU VAL VAL PRO GLU PRO VAL ALA ARG TRP SEQRES 7 B 280 SER ASN VAL GLN SER THR GLN ASP GLU PHE GLU GLU LEU SEQRES 8 B 280 THR MET SER GLN LYS ASN GLY GLY ASN VAL LEU GLN MET SEQRES 9 B 280 MET TYR GLU LYS PRO GLU ARG TRP SER PHE THR PHE GLN SEQRES 10 B 280 THR TYR ALA CYS LEU SER ARG ILE ARG ALA GLN LEU ALA SEQRES 11 B 280 SER LEU ASN GLY LYS LEU LYS ASP ALA GLU LYS PRO VAL SEQRES 12 B 280 LEU PHE PHE GLU ARG SER VAL TYR SER ASP ARG TYR ILE SEQRES 13 B 280 PHE ALA SER ASN LEU TYR GLU SER GLU SER MET ASN GLU SEQRES 14 B 280 THR GLU TRP THR ILE TYR GLN ASP TRP HIS ASP TRP MET SEQRES 15 B 280 ASN ASN GLN PHE GLY GLN SER LEU GLU LEU ASP GLY ILE SEQRES 16 B 280 ILE TYR LEU GLN ALA THR PRO GLU THR CYS LEU HIS ARG SEQRES 17 B 280 ILE TYR LEU ARG GLY ARG ASN GLU GLU GLN GLY ILE PRO SEQRES 18 B 280 LEU GLU TYR LEU GLU LYS LEU HIS TYR LYS HIS GLU SER SEQRES 19 B 280 TRP LEU LEU HIS ARG THR LEU LYS THR ASN PHE ASP TYR SEQRES 20 B 280 LEU GLN GLU VAL PRO ILE LEU THR LEU ASP VAL ASN GLU SEQRES 21 B 280 ASP PHE LYS ASP LYS TYR GLU SER LEU VAL GLU LYS VAL SEQRES 22 B 280 LYS GLU PHE LEU SER THR LEU HET ADP A 301 27 HET LTT A 302 15 HET ADP B 301 27 HET LTT B 302 15 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM LTT 4-AMINO-1-[(2S,4S)-2-(HYDROXYMETHYL)-1,3-DIOXOLAN-4- HETNAM 2 LTT YL]PYRIMIDIN-2(1H)-ONE HETSYN LTT (-)-L-2',3'-DIDEOXY-3'-OXACYTIDINE; TROXACITABINE; HETSYN 2 LTT TROXATYL FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 4 LTT 2(C8 H11 N3 O4) FORMUL 7 HOH *79(H2 O) HELIX 1 1 GLY A 33 LYS A 42 1 10 HELIX 2 2 GLN A 43 SER A 45 5 3 HELIX 3 3 PRO A 54 ASN A 60 1 7 HELIX 4 4 PHE A 68 THR A 72 5 5 HELIX 5 5 ASN A 80 LYS A 88 1 9 HELIX 6 6 LYS A 88 LYS A 115 1 28 HELIX 7 7 SER A 129 ILE A 136 1 8 HELIX 8 8 ILE A 136 SER A 144 1 9 HELIX 9 9 ASN A 148 GLY A 167 1 20 HELIX 10 10 THR A 181 GLY A 193 1 13 HELIX 11 11 ARG A 194 GLN A 198 5 5 HELIX 12 12 PRO A 201 LEU A 217 1 17 HELIX 13 13 PHE A 225 GLU A 230 5 6 HELIX 14 14 ASP A 241 ASP A 244 5 4 HELIX 15 15 LYS A 245 LEU A 260 1 16 HELIX 16 16 GLY B 33 LYS B 42 1 10 HELIX 17 17 GLN B 43 SER B 45 5 3 HELIX 18 18 PRO B 54 ASN B 60 1 7 HELIX 19 19 ASN B 80 LYS B 88 1 9 HELIX 20 20 LYS B 88 GLY B 114 1 27 HELIX 21 21 SER B 129 ILE B 136 1 8 HELIX 22 22 ILE B 136 SER B 144 1 9 HELIX 23 23 ASN B 148 GLY B 167 1 20 HELIX 24 24 THR B 181 GLY B 193 1 13 HELIX 25 25 ARG B 194 GLN B 198 5 5 HELIX 26 26 PRO B 201 LEU B 217 1 17 HELIX 27 27 PHE B 225 VAL B 231 5 7 HELIX 28 28 LYS B 245 LEU B 260 1 16 SHEET 1 A 5 TRP A 48 VAL A 51 0 SHEET 2 A 5 VAL A 123 GLU A 127 1 O PHE A 125 N GLU A 49 SHEET 3 A 5 LYS A 22 GLU A 27 1 N ILE A 26 O PHE A 126 SHEET 4 A 5 GLY A 174 GLN A 179 1 O ILE A 176 N SER A 25 SHEET 5 A 5 ILE A 233 ASP A 237 1 O LEU A 234 N TYR A 177 SHEET 1 B 5 TRP B 48 VAL B 51 0 SHEET 2 B 5 VAL B 123 GLU B 127 1 O PHE B 125 N GLU B 49 SHEET 3 B 5 LYS B 22 GLU B 27 1 N LYS B 22 O LEU B 124 SHEET 4 B 5 GLY B 174 GLN B 179 1 O ILE B 176 N GLU B 27 SHEET 5 B 5 ILE B 233 ASP B 237 1 O LEU B 234 N TYR B 177 SITE 1 AC1 17 ALA A 31 ALA A 32 GLY A 33 LYS A 34 SITE 2 AC1 17 SER A 35 THR A 36 ARG A 188 ARG A 192 SITE 3 AC1 17 GLU A 240 ASP A 241 PHE A 242 HOH A 314 SITE 4 AC1 17 HOH A 319 HOH A 326 HOH A 338 ASP B 241 SITE 5 AC1 17 PHE B 242 SITE 1 AC2 13 ILE A 30 GLU A 53 TRP A 58 LEU A 82 SITE 2 AC2 13 TYR A 86 PHE A 96 GLN A 97 ARG A 128 SITE 3 AC2 13 ASP A 133 PHE A 137 HOH A 308 HOH A 326 SITE 4 AC2 13 HOH A 350 SITE 1 AC3 16 ASP A 241 LYS A 243 ALA B 31 ALA B 32 SITE 2 AC3 16 GLY B 33 LYS B 34 SER B 35 THR B 36 SITE 3 AC3 16 ARG B 188 ARG B 192 GLU B 240 ASP B 241 SITE 4 AC3 16 PHE B 242 TYR B 246 HOH B 310 HOH B 329 SITE 1 AC4 9 GLU B 53 LEU B 82 TYR B 86 PHE B 96 SITE 2 AC4 9 GLN B 97 ARG B 128 ASP B 133 PHE B 137 SITE 3 AC4 9 HOH B 322 CRYST1 52.850 134.460 155.340 90.00 90.00 90.00 C 2 2 21 16 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 0.018921 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007437 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006437 0.00000 MASTER 501 0 4 28 10 0 16 6 0 0 0 44 END