HEADER TRANSFERASE 26-FEB-08 2VP0 TITLE STRUCTURAL STUDIES OF NUCLEOSIDE ANALOG AND FEEDBACK INHIBITOR BINDING TITLE 2 TO DROSOPHILA MELANOGASTER MULTISUBSTRATE DEOXYRIBONUCLEOSIDE KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYNUCLEOSIDE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DEOXYRIBONUCLEOSIDE KINASE, DM-DNK, MULTISPECIFIC COMPND 5 DEOXYNUCLEOSIDE KINASE; COMPND 6 EC: 2.7.1.145; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS ATP-BINDING, DNA SYNTHESIS, PHOSPHOPROTEIN, FEEDBACK INHIBITION, KEYWDS 2 DEOXYRIBONUCLEOSIDE KINASE, SALVAGE PATHWAY, NUCLEOTIDE-BINDING, KEYWDS 3 DTTP, KINASE, COMPLEX, DROSOPHILA, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR N.E.MIKKELSEN,B.MUNCH-PETERSEN,H.EKLUND REVDAT 4 13-DEC-23 2VP0 1 LINK REVDAT 3 24-FEB-09 2VP0 1 VERSN REVDAT 2 06-MAY-08 2VP0 1 JRNL REVDAT 1 29-APR-08 2VP0 0 JRNL AUTH N.E.MIKKELSEN,B.MUNCH-PETERSEN,H.EKLUND JRNL TITL STRUCTURAL STUDIES OF NUCLEOSIDE ANALOG AND FEEDBACK JRNL TITL 2 INHIBITOR BINDING TO DROSOPHILA MELANOGASTER MULTISUBSTRATE JRNL TITL 3 DEOXYRIBONUCLEOSIDE KINASE. JRNL REF FEBS J. V. 275 2151 2008 JRNL REFN ISSN 1742-464X JRNL PMID 18384378 JRNL DOI 10.1111/J.1742-4658.2008.06369.X REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 26365 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1394 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1922 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 95 REMARK 3 BIN FREE R VALUE : 0.2950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3280 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 123 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.74000 REMARK 3 B22 (A**2) : 1.57000 REMARK 3 B33 (A**2) : 0.17000 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): 0.253 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.211 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.144 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.531 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3416 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4630 ; 1.145 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 392 ; 5.585 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 168 ;35.306 ;23.929 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 626 ;14.894 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;19.859 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 496 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2544 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1585 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2267 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 203 ; 0.140 ; 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): 35 ; 0.156 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.268 ; 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): 2039 ; 0.624 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3204 ; 1.067 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1603 ; 1.551 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1426 ; 2.384 ; 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 2VP0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1290035445. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.981661 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26365 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1J90 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 59.52050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.48900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 59.52050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.48900 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.5 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 1 REMARK 465 ALA A 2 REMARK 465 GLU A 3 REMARK 465 ALA A 4 REMARK 465 ALA A 5 REMARK 465 SER A 6 REMARK 465 CYS A 7 REMARK 465 ALA A 8 REMARK 465 ARG A 9 REMARK 465 LYS A 10 REMARK 465 GLY A 11 REMARK 465 LEU A 209 REMARK 465 ASN A 210 REMARK 465 LEU A 211 REMARK 465 GLU A 212 REMARK 465 ASN A 213 REMARK 465 ILE A 214 REMARK 465 GLY A 215 REMARK 465 THR A 216 REMARK 465 GLU A 217 REMARK 465 TYR A 218 REMARK 465 GLN A 219 REMARK 465 ARG A 220 REMARK 465 SER A 221 REMARK 465 GLU A 222 REMARK 465 SER A 223 REMARK 465 SER A 224 REMARK 465 ILE A 225 REMARK 465 PHE A 226 REMARK 465 ASP A 227 REMARK 465 ALA A 228 REMARK 465 ILE A 229 REMARK 465 SER A 230 REMARK 465 SER A 231 REMARK 465 ASN A 232 REMARK 465 GLN A 233 REMARK 465 GLN A 234 REMARK 465 PRO A 235 REMARK 465 SER A 236 REMARK 465 PRO A 237 REMARK 465 VAL A 238 REMARK 465 LEU A 239 REMARK 465 VAL A 240 REMARK 465 SER A 241 REMARK 465 PRO A 242 REMARK 465 SER A 243 REMARK 465 LYS A 244 REMARK 465 ARG A 245 REMARK 465 GLN A 246 REMARK 465 ARG A 247 REMARK 465 VAL A 248 REMARK 465 ALA A 249 REMARK 465 ARG A 250 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLU B 3 REMARK 465 ALA B 4 REMARK 465 ALA B 5 REMARK 465 SER B 6 REMARK 465 CYS B 7 REMARK 465 ALA B 8 REMARK 465 ARG B 9 REMARK 465 LYS B 10 REMARK 465 GLY B 11 REMARK 465 LEU B 209 REMARK 465 ASN B 210 REMARK 465 LEU B 211 REMARK 465 GLU B 212 REMARK 465 ASN B 213 REMARK 465 ILE B 214 REMARK 465 GLY B 215 REMARK 465 THR B 216 REMARK 465 GLU B 217 REMARK 465 TYR B 218 REMARK 465 GLN B 219 REMARK 465 ARG B 220 REMARK 465 SER B 221 REMARK 465 GLU B 222 REMARK 465 SER B 223 REMARK 465 SER B 224 REMARK 465 ILE B 225 REMARK 465 PHE B 226 REMARK 465 ASP B 227 REMARK 465 ALA B 228 REMARK 465 ILE B 229 REMARK 465 SER B 230 REMARK 465 SER B 231 REMARK 465 ASN B 232 REMARK 465 GLN B 233 REMARK 465 GLN B 234 REMARK 465 PRO B 235 REMARK 465 SER B 236 REMARK 465 PRO B 237 REMARK 465 VAL B 238 REMARK 465 LEU B 239 REMARK 465 VAL B 240 REMARK 465 SER B 241 REMARK 465 PRO B 242 REMARK 465 SER B 243 REMARK 465 LYS B 244 REMARK 465 ARG B 245 REMARK 465 GLN B 246 REMARK 465 ARG B 247 REMARK 465 VAL B 248 REMARK 465 ALA B 249 REMARK 465 ARG B 250 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 SER A 199 O CYS A 200 1.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP A 46 OH TYR B 43 4456 2.15 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 ARG A 105 -178.49 64.76 REMARK 500 PRO A 197 -91.27 -27.83 REMARK 500 GLN A 198 -86.08 -95.66 REMARK 500 SER A 199 72.77 45.04 REMARK 500 CYS A 200 -167.55 -0.44 REMARK 500 ALA B 15 -0.21 71.63 REMARK 500 LYS B 44 -35.37 -39.69 REMARK 500 ASN B 59 82.74 -154.58 REMARK 500 ARG B 105 178.10 70.06 REMARK 500 CYS B 113 -65.88 -104.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1209 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 34 OG1 REMARK 620 2 GLU A 52 OE2 86.8 REMARK 620 3 GLU A 104 OE2 84.9 99.9 REMARK 620 4 TTP A1210 O2G 101.1 159.8 99.3 REMARK 620 5 TTP A1210 O1B 165.7 80.1 103.0 89.5 REMARK 620 6 HOH A2007 O 84.5 77.7 169.3 84.5 87.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1209 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 34 OG1 REMARK 620 2 GLU B 52 OE1 79.6 REMARK 620 3 GLU B 104 OE2 77.1 104.1 REMARK 620 4 TTP B1210 O1B 169.8 92.9 111.7 REMARK 620 5 TTP B1210 O3G 88.1 154.4 94.8 95.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TTP A1210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TTP B1210 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZM7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D. MELANOGASTER DEOXYRIBONUCLEOSIDEKINASE REMARK 900 MUTANT N64D IN COMPLEX WITH DTTP REMARK 900 RELATED ID: 2JCS RELATED DB: PDB REMARK 900 ACTIVE SITE MUTANT OF DNK FROM D. MELANOGASTER WITH DTTP BOUND REMARK 900 RELATED ID: 1OT3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DROSOPHILA DEOXYRIBONUCLEOTIDE KINASECOMPLEXED REMARK 900 WITH THE SUBSTRATE DEOXYTHYMIDINE REMARK 900 RELATED ID: 1OE0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DROSOPHILA DEOXYRIBONUCLEOSIDE KINASE IN REMARK 900 COMPLEX WITH DTTP REMARK 900 RELATED ID: 1ZMX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D. MELANOGASTER DEOXYRIBONUCLEOSIDEKINASE N64D REMARK 900 MUTANT IN COMPLEX WITH THYMIDINE REMARK 900 RELATED ID: 1J90 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DROSOPHILA DEOXYRIBONUCLEOSIDE KINASE DBREF 2VP0 A 1 250 UNP Q9XZT6 DNK_DROME 1 250 DBREF 2VP0 B 1 250 UNP Q9XZT6 DNK_DROME 1 250 SEQRES 1 A 250 MET ALA GLU ALA ALA SER CYS ALA ARG LYS GLY THR LYS SEQRES 2 A 250 TYR ALA GLU GLY THR GLN PRO PHE THR VAL LEU ILE GLU SEQRES 3 A 250 GLY ASN ILE GLY SER GLY LYS THR THR TYR LEU ASN HIS SEQRES 4 A 250 PHE GLU LYS TYR LYS ASN ASP ILE CYS LEU LEU THR GLU SEQRES 5 A 250 PRO VAL GLU LYS TRP ARG ASN VAL ASN GLY VAL ASN LEU SEQRES 6 A 250 LEU GLU LEU MET TYR LYS ASP PRO LYS LYS TRP ALA MET SEQRES 7 A 250 PRO PHE GLN SER TYR VAL THR LEU THR MET LEU GLN SER SEQRES 8 A 250 HIS THR ALA PRO THR ASN LYS LYS LEU LYS ILE MET GLU SEQRES 9 A 250 ARG SER ILE PHE SER ALA ARG TYR CYS PHE VAL GLU ASN SEQRES 10 A 250 MET ARG ARG ASN GLY SER LEU GLU GLN GLY MET TYR ASN SEQRES 11 A 250 THR LEU GLU GLU TRP TYR LYS PHE ILE GLU GLU SER ILE SEQRES 12 A 250 HIS VAL GLN ALA ASP LEU ILE ILE TYR LEU ARG THR SER SEQRES 13 A 250 PRO GLU VAL ALA TYR GLU ARG ILE ARG GLN ARG ALA ARG SEQRES 14 A 250 SER GLU GLU SER CYS VAL PRO LEU LYS TYR LEU GLN GLU SEQRES 15 A 250 LEU HIS GLU LEU HIS GLU ASP TRP LEU ILE HIS GLN ARG SEQRES 16 A 250 ARG PRO GLN SER CYS LYS VAL LEU VAL LEU ASP ALA ASP SEQRES 17 A 250 LEU ASN LEU GLU ASN ILE GLY THR GLU TYR GLN ARG SER SEQRES 18 A 250 GLU SER SER ILE PHE ASP ALA ILE SER SER ASN GLN GLN SEQRES 19 A 250 PRO SER PRO VAL LEU VAL SER PRO SER LYS ARG GLN ARG SEQRES 20 A 250 VAL ALA ARG SEQRES 1 B 250 MET ALA GLU ALA ALA SER CYS ALA ARG LYS GLY THR LYS SEQRES 2 B 250 TYR ALA GLU GLY THR GLN PRO PHE THR VAL LEU ILE GLU SEQRES 3 B 250 GLY ASN ILE GLY SER GLY LYS THR THR TYR LEU ASN HIS SEQRES 4 B 250 PHE GLU LYS TYR LYS ASN ASP ILE CYS LEU LEU THR GLU SEQRES 5 B 250 PRO VAL GLU LYS TRP ARG ASN VAL ASN GLY VAL ASN LEU SEQRES 6 B 250 LEU GLU LEU MET TYR LYS ASP PRO LYS LYS TRP ALA MET SEQRES 7 B 250 PRO PHE GLN SER TYR VAL THR LEU THR MET LEU GLN SER SEQRES 8 B 250 HIS THR ALA PRO THR ASN LYS LYS LEU LYS ILE MET GLU SEQRES 9 B 250 ARG SER ILE PHE SER ALA ARG TYR CYS PHE VAL GLU ASN SEQRES 10 B 250 MET ARG ARG ASN GLY SER LEU GLU GLN GLY MET TYR ASN SEQRES 11 B 250 THR LEU GLU GLU TRP TYR LYS PHE ILE GLU GLU SER ILE SEQRES 12 B 250 HIS VAL GLN ALA ASP LEU ILE ILE TYR LEU ARG THR SER SEQRES 13 B 250 PRO GLU VAL ALA TYR GLU ARG ILE ARG GLN ARG ALA ARG SEQRES 14 B 250 SER GLU GLU SER CYS VAL PRO LEU LYS TYR LEU GLN GLU SEQRES 15 B 250 LEU HIS GLU LEU HIS GLU ASP TRP LEU ILE HIS GLN ARG SEQRES 16 B 250 ARG PRO GLN SER CYS LYS VAL LEU VAL LEU ASP ALA ASP SEQRES 17 B 250 LEU ASN LEU GLU ASN ILE GLY THR GLU TYR GLN ARG SER SEQRES 18 B 250 GLU SER SER ILE PHE ASP ALA ILE SER SER ASN GLN GLN SEQRES 19 B 250 PRO SER PRO VAL LEU VAL SER PRO SER LYS ARG GLN ARG SEQRES 20 B 250 VAL ALA ARG HET MG A1209 1 HET TTP A1210 29 HET MG B1209 1 HET TTP B1210 29 HETNAM MG MAGNESIUM ION HETNAM TTP THYMIDINE-5'-TRIPHOSPHATE FORMUL 3 MG 2(MG 2+) FORMUL 4 TTP 2(C10 H17 N2 O14 P3) FORMUL 7 HOH *123(H2 O) HELIX 1 1 GLY A 32 HIS A 39 1 8 HELIX 2 2 PHE A 40 LYS A 44 5 5 HELIX 3 3 PRO A 53 ARG A 58 1 6 HELIX 4 4 ASN A 64 ASP A 72 1 9 HELIX 5 5 ASP A 72 THR A 93 1 22 HELIX 6 6 SER A 106 CYS A 113 1 8 HELIX 7 7 CYS A 113 ASN A 121 1 9 HELIX 8 8 GLU A 125 ILE A 143 1 19 HELIX 9 9 SER A 156 ALA A 168 1 13 HELIX 10 10 ARG A 169 SER A 173 5 5 HELIX 11 11 PRO A 176 ILE A 192 1 17 HELIX 12 12 GLY B 32 HIS B 39 1 8 HELIX 13 13 PHE B 40 LYS B 44 5 5 HELIX 14 14 PRO B 53 ARG B 58 1 6 HELIX 15 15 ASN B 64 ASP B 72 1 9 HELIX 16 16 ASP B 72 THR B 93 1 22 HELIX 17 17 SER B 106 CYS B 113 1 8 HELIX 18 18 CYS B 113 ASN B 121 1 9 HELIX 19 19 GLU B 125 ILE B 143 1 19 HELIX 20 20 SER B 156 ALA B 168 1 13 HELIX 21 21 ARG B 169 SER B 173 5 5 HELIX 22 22 PRO B 176 ILE B 192 1 17 SHEET 1 AA 5 CYS A 48 LEU A 50 0 SHEET 2 AA 5 LEU A 100 GLU A 104 1 O LEU A 100 N CYS A 48 SHEET 3 AA 5 PHE A 21 GLU A 26 1 O PHE A 21 N LYS A 101 SHEET 4 AA 5 LEU A 149 ARG A 154 1 O LEU A 149 N LEU A 24 SHEET 5 AA 5 LYS A 201 ASP A 206 1 O LYS A 201 N ILE A 150 SHEET 1 BA 5 ILE B 47 LEU B 50 0 SHEET 2 BA 5 LEU B 100 GLU B 104 1 O LEU B 100 N CYS B 48 SHEET 3 BA 5 PHE B 21 GLU B 26 1 O PHE B 21 N LYS B 101 SHEET 4 BA 5 LEU B 149 ARG B 154 1 O LEU B 149 N LEU B 24 SHEET 5 BA 5 LYS B 201 ASP B 206 1 O LYS B 201 N ILE B 150 LINK OG1 THR A 34 MG MG A1209 1555 1555 2.17 LINK OE2 GLU A 52 MG MG A1209 1555 1555 2.36 LINK OE2 GLU A 104 MG MG A1209 1555 1555 2.38 LINK MG MG A1209 O2G TTP A1210 1555 1555 2.13 LINK MG MG A1209 O1B TTP A1210 1555 1555 2.25 LINK MG MG A1209 O HOH A2007 1555 1555 2.08 LINK OG1 THR B 34 MG MG B1209 1555 1555 2.14 LINK OE1 GLU B 52 MG MG B1209 1555 1555 2.14 LINK OE2 GLU B 104 MG MG B1209 1555 1555 2.38 LINK MG MG B1209 O1B TTP B1210 1555 1555 1.88 LINK MG MG B1209 O3G TTP B1210 1555 1555 2.16 SITE 1 AC1 5 THR A 34 GLU A 52 GLU A 104 TTP A1210 SITE 2 AC1 5 HOH A2007 SITE 1 AC2 4 THR B 34 GLU B 52 GLU B 104 TTP B1210 SITE 1 AC3 28 ILE A 29 GLY A 30 SER A 31 GLY A 32 SITE 2 AC3 28 LYS A 33 THR A 34 GLU A 52 VAL A 54 SITE 3 AC3 28 TRP A 57 LEU A 66 MET A 69 TYR A 70 SITE 4 AC3 28 PHE A 80 GLN A 81 VAL A 84 GLU A 104 SITE 5 AC3 28 ARG A 105 ALA A 110 PHE A 114 ARG A 167 SITE 6 AC3 28 ARG A 169 GLU A 172 MG A1209 HOH A2007 SITE 7 AC3 28 HOH A2058 HOH A2071 HOH A2072 HOH A2073 SITE 1 AC4 25 ILE B 29 GLY B 30 SER B 31 GLY B 32 SITE 2 AC4 25 LYS B 33 THR B 34 GLU B 52 TRP B 57 SITE 3 AC4 25 LEU B 66 MET B 69 TYR B 70 PHE B 80 SITE 4 AC4 25 GLN B 81 GLU B 104 ARG B 105 ALA B 110 SITE 5 AC4 25 PHE B 114 ARG B 167 ARG B 169 GLU B 172 SITE 6 AC4 25 MG B1209 HOH B2042 HOH B2048 HOH B2049 SITE 7 AC4 25 HOH B2050 CRYST1 119.041 64.978 69.109 90.00 90.00 90.00 P 21 21 2 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 0.008400 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015390 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014470 0.00000 MTRIX1 1 -0.986600 -0.004479 -0.162900 32.05000 1 MTRIX2 1 -0.007881 -0.997100 0.075130 29.67000 1 MTRIX3 1 -0.162800 0.075410 0.983800 1.48800 1