10 20 30 40 50 60 70 80 2NO7 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE 25-OCT-06 2NO7
TITLE C4S DCK VARIANT OF DCK IN COMPLEX WITH L-DC+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, HUMAN DEOXYCYTIDINE KINASE, L-DC, ENANTIOMER, KEYWDS 2 ENANTIOSELECTIVITY, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR E.SABINI,S.HAZRA,M.KONRAD,S.K.BURLEY,A.LAVIE
REVDAT 2 24-FEB-09 2NO7 1 VERSN REVDAT 1 03-JUL-07 2NO7 0
JRNL AUTH E.SABINI,S.HAZRA,M.KONRAD,A.LAVIE JRNL TITL NONENANTIOSELECTIVITY PROPERTY OF HUMAN JRNL TITL 2 DEOXYCYTIDINE KINASE EXPLAINED BY STRUCTURES OF JRNL TITL 3 THE ENZYME IN COMPLEX WITH L- AND 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 1
REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON 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) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 51646 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5763 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) : 3105 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE SET COUNT : 329 REMARK 3 BIN FREE R VALUE : 0.3690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3813 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 289 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.14000 REMARK 3 B22 (A**2) : -0.10000 REMARK 3 B33 (A**2) : -0.05000 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): 0.119 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.124 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.791 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3999 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5432 ; 1.780 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 455 ; 5.577 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 203 ;40.232 ;24.532 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 682 ;15.657 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;17.405 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 584 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3030 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1801 ; 0.208 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2734 ; 0.313 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 324 ; 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): 68 ; 0.265 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.193 ; 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): 2354 ; 1.231 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3711 ; 1.914 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1929 ; 2.766 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1718 ; 4.061 ; 4.500 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 2NO7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-06. REMARK 100 THE RCSB ID CODE IS RCSB040102.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-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 : 57715 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 94.3 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.3000 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) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.55100 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: 1P5Z REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 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 78.02000 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 78.02000 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 26.40000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 66.67500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.40000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 66.67500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 78.02000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.40000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.67500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 78.02000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.40000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 66.67500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA.
REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 -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 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 ASN B 77 REMARK 465 LYS B 115 REMARK 465 LEU B 116 REMARK 465 LYS B 117 REMARK 465 GLY B 167 REMARK 465 GLN B 168 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 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 ARG B 20 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 22 CG CD CE NZ REMARK 470 ASN B 113 CG OD1 ND2 REMARK 470 ASP B 118 CB CG OD1 OD2 REMARK 470 LYS B 121 CG CD CE NZ REMARK 470 LYS B 222 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 447 O HOH A 464 2.15 REMARK 500 O HOH A 499 O HOH B 463 2.16 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 48.75 -77.97 REMARK 500 ARG A 128 176.76 65.15 REMARK 500 ILE A 136 -70.66 -111.51 REMARK 500 GLN A 165 -71.83 -78.21 REMARK 500 PHE A 166 48.96 -98.23 REMARK 500 ARG B 128 173.42 61.92 REMARK 500 ILE B 136 -69.53 -106.93 REMARK 500 ASN B 224 30.97 -89.47 REMARK 500 GLU B 247 -58.83 -26.24 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 495 DISTANCE = 6.00 ANGSTROMS
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 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 301 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LDC A 401 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LDC B 401
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1P5Z RELATED DB: PDB REMARK 900 WILD TYPE HUMAN DEOXYCYTIDINE KINASE IN COMPLEX WITH REMARK 900 CYTARABINE AND ADP-MG REMARK 900 RELATED ID: 1P60 RELATED DB: PDB REMARK 900 WILD TYPE HUMAN DEOXYCYTIDINE KINASE IN COMPLEX WITH REMARK 900 DEOXYCYTIDINE AND ADP REMARK 900 RELATED ID: 1P61 RELATED DB: PDB REMARK 900 WILD TYPE HUMAN DEOXYCYTIDINE KINASE IN COMPLEX WITH REMARK 900 DEOXYCYTIDINE AND ADP REMARK 900 RELATED ID: 1P62 RELATED DB: PDB REMARK 900 WILD TYPE HUMAN DEOXYCYTIDINE KINASE IN COMPLEX WITH REMARK 900 GEMCITABINE AND ADP-MG REMARK 900 RELATED ID: 2A2Z RELATED DB: PDB REMARK 900 INSERT-DELETION MUTANT OF HUMAN DEOXYCYTIDINE KINASE IN REMARK 900 COMPLEX WITH DEOXYCYTIDINE AND UDP REMARK 900 RELATED ID: 2A30 RELATED DB: PDB REMARK 900 INSERT-DELETION MUTANT OF HUMAN DEOXYCYTIDINE KINASE IN REMARK 900 COMPLEX 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: 2NO9 RELATED DB: PDB REMARK 900 RELATED ID: 2NOA RELATED DB: PDB
DBREF 2NO7 A 1 260 UNP P27707 DCK_HUMAN 1 260 DBREF 2NO7 B 1 260 UNP P27707 DCK_HUMAN 1 260
SEQADV 2NO7 MET A -19 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 GLY A -18 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 SER A -17 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 SER A -16 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 HIS A -15 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 HIS A -14 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 HIS A -13 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 HIS A -12 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 HIS A -11 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 HIS A -10 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 SER A -9 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 SER A -8 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 GLY A -7 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 LEU A -6 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 VAL A -5 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 PRO A -4 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 ARG A -3 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 GLY A -2 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 SER A -1 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 HIS A 0 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 SER A 9 UNP P27707 CYS 9 ENGINEERED SEQADV 2NO7 SER A 45 UNP P27707 CYS 45 ENGINEERED SEQADV 2NO7 SER A 59 UNP P27707 CYS 59 ENGINEERED SEQADV 2NO7 SER A 146 UNP P27707 CYS 146 ENGINEERED SEQADV 2NO7 MET B -19 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 GLY B -18 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 SER B -17 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 SER B -16 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 HIS B -15 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 HIS B -14 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 HIS B -13 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 HIS B -12 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 HIS B -11 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 HIS B -10 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 SER B -9 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 SER B -8 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 GLY B -7 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 LEU B -6 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 VAL B -5 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 PRO B -4 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 ARG B -3 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 GLY B -2 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 SER B -1 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 HIS B 0 UNP P27707 CLONING ARTIFACT SEQADV 2NO7 SER B 9 UNP P27707 CYS 9 ENGINEERED SEQADV 2NO7 SER B 45 UNP P27707 CYS 45 ENGINEERED SEQADV 2NO7 SER B 59 UNP P27707 CYS 59 ENGINEERED SEQADV 2NO7 SER B 146 UNP P27707 CYS 146 ENGINEERED
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 ADP B 301 27 HET LDC A 401 16 HET LDC B 401 16
HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM LDC 4-AMINO-1-(2-DEOXY-BETA-L-ERYTHRO-PENTOFURANOSYL) HETNAM 2 LDC PYRIMIDIN-2(1H)-ONE
HETSYN LDC L-2'-DEOXYCYTIDINE
FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 5 LDC 2(C9 H13 N3 O4) FORMUL 7 HOH *289(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 MET A 73 1 6 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 PHE A 166 1 19 HELIX 10 10 GLY A 167 GLU A 171 5 5 HELIX 11 11 THR A 181 GLY A 193 1 13 HELIX 12 12 ARG A 194 GLN A 198 5 5 HELIX 13 13 PRO A 201 LEU A 217 1 17 HELIX 14 14 PHE A 225 GLU A 230 5 6 HELIX 15 15 ASP A 241 SER A 258 1 18 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 PHE B 166 1 19 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 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 GLU A 49 SHEET 3 A 5 LYS A 22 GLU A 27 1 N LYS A 22 O LEU A 124 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 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 LYS B 22 O LEU B 124 SHEET 4 B 5 GLY B 174 GLN B 179 1 O ILE B 176 N SER B 25 SHEET 5 B 5 ILE B 233 ASP B 237 1 O LEU B 236 N GLN B 179
SITE 1 AC1 19 ALA A 31 ALA A 32 GLY A 33 LYS A 34 SITE 2 AC1 19 SER A 35 THR A 36 ARG A 188 ARG A 192 SITE 3 AC1 19 GLU A 240 ASP A 241 PHE A 242 HOH A 429 SITE 4 AC1 19 HOH A 484 HOH A 512 HOH A 520 HOH A 522 SITE 5 AC1 19 HOH A 540 ASP B 241 PHE B 242 SITE 1 AC2 21 ASP A 241 LYS A 243 ALA B 31 ALA B 32 SITE 2 AC2 21 GLY B 33 LYS B 34 SER B 35 THR B 36 SITE 3 AC2 21 ARG B 188 ARG B 192 GLU B 240 ASP B 241 SITE 4 AC2 21 PHE B 242 TYR B 246 HOH B 447 HOH B 458 SITE 5 AC2 21 HOH B 490 HOH B 510 HOH B 517 HOH B 520 SITE 6 AC2 21 HOH B 523 SITE 1 AC3 15 ILE A 30 GLU A 53 LEU A 82 MET A 85 SITE 2 AC3 15 TYR A 86 PHE A 96 GLN A 97 ARG A 128 SITE 3 AC3 15 ASP A 133 PHE A 137 GLU A 197 HOH A 449 SITE 4 AC3 15 HOH A 512 HOH A 522 HOH A 535 SITE 1 AC4 15 GLU B 53 VAL B 55 LEU B 82 TYR B 86 SITE 2 AC4 15 PHE B 96 GLN B 97 ARG B 128 ASP B 133 SITE 3 AC4 15 PHE B 137 ARG B 194 GLU B 197 HOH B 483 SITE 4 AC4 15 HOH B 490 HOH B 517 HOH B 532
CRYST1 52.800 133.350 156.040 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 0.018939 0.000000 0.000000 0.00000
SCALE2 0.000000 0.007499 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006409 0.00000