HEADER TRANSFERASE 24-OCT-06 2NO0 TITLE C4S DCK VARIANT OF DCK IN COMPLEX WITH GEMCITABINE+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, GEMCITABINE, HUMAN DEOXYCYTIDINE KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR E.SABINI,S.HAZRA,M.KONRAD,S.K.BURLEY,A.LAVIE REVDAT 6 30-AUG-23 2NO0 1 REMARK REVDAT 5 20-OCT-21 2NO0 1 SEQADV REVDAT 4 03-FEB-21 2NO0 1 AUTHOR REMARK REVDAT 3 11-OCT-17 2NO0 1 REMARK REVDAT 2 24-FEB-09 2NO0 1 VERSN REVDAT 1 03-JUL-07 2NO0 0 JRNL AUTH E.SABINI,S.HAZRA,M.KONRAD,A.LAVIE JRNL TITL NONENANTIOSELECTIVITY PROPERTY OF HUMAN DEOXYCYTIDINE KINASE JRNL TITL 2 EXPLAINED BY STRUCTURES OF THE ENZYME IN COMPLEX WITH L- AND JRNL TITL 3 D-NUCLEOSIDES. JRNL REF J.MED.CHEM. V. 50 3004 2007 JRNL REFN ISSN 0022-2623 JRNL PMID 17530837 JRNL DOI 10.1021/JM0700215 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 45728 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) : 0.173 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 5123 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3193 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 336 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3862 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 267 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.18000 REMARK 3 B22 (A**2) : -0.22000 REMARK 3 B33 (A**2) : 0.40000 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): 0.124 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.120 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.338 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4074 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5534 ; 1.585 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 462 ; 5.278 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 209 ;38.291 ;24.593 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 708 ;14.087 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;19.074 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 593 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3087 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1856 ; 0.201 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2792 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 299 ; 0.146 ; 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): 71 ; 0.235 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.189 ; 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): 2398 ; 1.134 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3769 ; 1.795 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1971 ; 2.775 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1763 ; 4.016 ; 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 2NO0 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_1000040095. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-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 : 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 : 50852 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07400 REMARK 200 FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36300 REMARK 200 FOR SHELL : 4.700 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 (%): 44.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 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 78.65000 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 78.65000 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 26.15000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 66.20000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.15000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 66.20000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 78.65000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.15000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.20000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 78.65000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.15000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 66.20000 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: 5230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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: 10390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 132.40000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 157.30000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 26.15000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 -66.20000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 26.15000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 198.60000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 157.30000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 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 132.40000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 157.30000 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 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 LYS B 117 REMARK 465 LYS B 243 REMARK 465 ASP B 244 REMARK 465 LYS B 245 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 A 76 CG CD CE NZ REMARK 470 LYS A 117 CG CD CE NZ REMARK 470 ASP A 118 CB CG OD1 OD2 REMARK 470 LYS A 121 CG CD CE NZ REMARK 470 GLN A 229 CG CD OE1 NE2 REMARK 470 GLU A 251 CG CD OE1 OE2 REMARK 470 ASN B 113 CG OD1 ND2 REMARK 470 LYS B 115 CB CG CD CE NZ REMARK 470 ASP B 118 CB CG OD1 OD2 REMARK 470 LYS B 222 CG CD CE NZ 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 ARG A 104 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 106 NE - CZ - NH2 ANGL. DEV. = -3.1 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 PRO A 54 43.94 -74.27 REMARK 500 ARG A 128 172.59 66.96 REMARK 500 ILE A 136 -66.75 -104.34 REMARK 500 PRO B 54 47.10 -73.87 REMARK 500 ARG B 128 175.98 65.06 REMARK 500 ILE B 136 -69.35 -106.89 REMARK 500 LEU B 217 -60.39 -109.35 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 GEO 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 GEO 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: 2NO1 RELATED DB: PDB DBREF 2NO0 A 1 260 UNP P27707 DCK_HUMAN 1 260 DBREF 2NO0 B 1 260 UNP P27707 DCK_HUMAN 1 260 SEQADV 2NO0 MET A -19 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 GLY A -18 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 SER A -17 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 SER A -16 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 HIS A -15 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 HIS A -14 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 HIS A -13 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 HIS A -12 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 HIS A -11 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 HIS A -10 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 SER A -9 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 SER A -8 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 GLY A -7 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 LEU A -6 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 VAL A -5 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 PRO A -4 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 ARG A -3 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 GLY A -2 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 SER A -1 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 HIS A 0 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 SER A 9 UNP P27707 CYS 9 ENGINEERED MUTATION SEQADV 2NO0 SER A 45 UNP P27707 CYS 45 ENGINEERED MUTATION SEQADV 2NO0 SER A 59 UNP P27707 CYS 59 ENGINEERED MUTATION SEQADV 2NO0 SER A 146 UNP P27707 CYS 146 ENGINEERED MUTATION SEQADV 2NO0 MET B -19 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 GLY B -18 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 SER B -17 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 SER B -16 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 HIS B -15 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 HIS B -14 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 HIS B -13 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 HIS B -12 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 HIS B -11 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 HIS B -10 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 SER B -9 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 SER B -8 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 GLY B -7 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 LEU B -6 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 VAL B -5 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 PRO B -4 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 ARG B -3 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 GLY B -2 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 SER B -1 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 HIS B 0 UNP P27707 CLONING ARTIFACT SEQADV 2NO0 SER B 9 UNP P27707 CYS 9 ENGINEERED MUTATION SEQADV 2NO0 SER B 45 UNP P27707 CYS 45 ENGINEERED MUTATION SEQADV 2NO0 SER B 59 UNP P27707 CYS 59 ENGINEERED MUTATION SEQADV 2NO0 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 GEO A 302 18 HET ADP B 301 27 HET GEO B 302 18 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM GEO GEMCITABINE HETSYN GEO 2',2'-DIFLUORODEOXYCYTIDINE FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 4 GEO 2(C9 H11 F2 N3 O4) FORMUL 7 HOH *267(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 GLU A 171 1 24 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 SER A 258 1 18 HELIX 15 15 GLY B 33 LYS B 42 1 10 HELIX 16 16 GLN B 43 SER B 45 5 3 HELIX 17 17 PRO B 54 ASN B 60 1 7 HELIX 18 18 ASN B 80 LYS B 88 1 9 HELIX 19 19 LYS B 88 LYS B 115 1 28 HELIX 20 20 SER B 129 ILE B 136 1 8 HELIX 21 21 ILE B 136 SER B 144 1 9 HELIX 22 22 ASN B 148 GLU B 171 1 24 HELIX 23 23 THR B 181 GLY B 193 1 13 HELIX 24 24 ARG B 194 GLN B 198 5 5 HELIX 25 25 PRO B 201 LEU B 217 1 17 HELIX 26 26 PHE B 225 VAL B 231 5 7 HELIX 27 27 TYR B 246 THR B 259 1 14 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 VAL A 51 SHEET 3 A 5 LYS A 22 GLY A 28 1 N ILE A 26 O PHE A 126 SHEET 4 A 5 GLY A 174 GLN A 179 1 O LEU A 178 N GLU A 27 SHEET 5 A 5 ILE A 233 ASP A 237 1 O LEU A 236 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 VAL B 51 SHEET 3 B 5 LYS B 22 GLU B 27 1 N ILE B 26 O PHE B 126 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 236 N TYR B 177 SITE 1 AC1 18 ALA A 31 ALA A 32 GLY A 33 LYS A 34 SITE 2 AC1 18 SER A 35 THR A 36 ARG A 188 ARG A 192 SITE 3 AC1 18 GLU A 240 ASP A 241 PHE A 242 HOH A 339 SITE 4 AC1 18 HOH A 370 HOH A 396 HOH A 398 HOH A 421 SITE 5 AC1 18 ASP B 241 PHE B 242 SITE 1 AC2 14 ILE A 30 GLU A 53 TRP A 58 MET A 85 SITE 2 AC2 14 TYR A 86 PHE A 96 GLN A 97 ARG A 128 SITE 3 AC2 14 ASP A 133 PHE A 137 GLU A 197 HOH A 373 SITE 4 AC2 14 HOH A 398 HOH A 419 SITE 1 AC3 20 ASP A 241 LYS A 243 HOH A 344 HOH A 421 SITE 2 AC3 20 ALA B 31 ALA B 32 GLY B 33 LYS B 34 SITE 3 AC3 20 SER B 35 THR B 36 ARG B 188 ARG B 192 SITE 4 AC3 20 GLU B 240 ASP B 241 PHE B 242 TYR B 246 SITE 5 AC3 20 HOH B 395 HOH B 398 HOH B 404 HOH B 408 SITE 1 AC4 14 ILE B 30 GLU B 53 TRP B 58 LEU B 82 SITE 2 AC4 14 MET B 85 TYR B 86 PHE B 96 GLN B 97 SITE 3 AC4 14 ARG B 128 ASP B 133 PHE B 137 GLU B 197 SITE 4 AC4 14 HOH B 404 HOH B 406 CRYST1 52.300 132.400 157.300 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 0.019120 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007553 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006357 0.00000