HEADER TRANSFERASE 26-FEB-08 2VP4 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, C, D; COMPND 4 FRAGMENT: RESIDUES 1-230; COMPND 5 SYNONYM: DEOXYRIBONUCLEOSIDE KINASE, DM-DNK, MULTISPECIFIC COMPND 6 DEOXYNUCLEOSIDE KINASE; COMPND 7 EC: 2.7.1.145; COMPND 8 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 2VP4 1 REMARK REVDAT 3 24-FEB-09 2VP4 1 VERSN REVDAT 2 06-MAY-08 2VP4 1 JRNL REVDAT 1 29-APR-08 2VP4 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) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 53215 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2850 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) : 3917 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE SET COUNT : 203 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6592 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 112 REMARK 3 SOLVENT ATOMS : 459 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.28000 REMARK 3 B22 (A**2) : -2.08000 REMARK 3 B33 (A**2) : 0.94000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.60000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.237 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.205 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.156 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.047 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 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): 6860 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9296 ; 1.403 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 788 ; 6.144 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 338 ;34.314 ;23.964 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1258 ;16.304 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 48 ;17.626 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 998 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5108 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3250 ; 0.197 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4568 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 506 ; 0.147 ; 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): 39 ; 0.355 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.413 ; 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): 4104 ; 0.724 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6440 ; 1.209 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3211 ; 1.816 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2856 ; 2.739 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2VP4 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_1290035449. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-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 : 53215 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1J90 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 59.51700 REMARK 290 SMTRY3 2 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 8300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 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 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 MET C 1 REMARK 465 ALA C 2 REMARK 465 GLU C 3 REMARK 465 ALA C 4 REMARK 465 ALA C 5 REMARK 465 SER C 6 REMARK 465 CYS C 7 REMARK 465 ALA C 8 REMARK 465 ARG C 9 REMARK 465 LYS C 10 REMARK 465 GLY C 11 REMARK 465 LEU C 209 REMARK 465 ASN C 210 REMARK 465 LEU C 211 REMARK 465 GLU C 212 REMARK 465 ASN C 213 REMARK 465 ILE C 214 REMARK 465 GLY C 215 REMARK 465 THR C 216 REMARK 465 GLU C 217 REMARK 465 TYR C 218 REMARK 465 GLN C 219 REMARK 465 ARG C 220 REMARK 465 SER C 221 REMARK 465 GLU C 222 REMARK 465 SER C 223 REMARK 465 SER C 224 REMARK 465 ILE C 225 REMARK 465 PHE C 226 REMARK 465 ASP C 227 REMARK 465 ALA C 228 REMARK 465 ILE C 229 REMARK 465 SER C 230 REMARK 465 MET D 1 REMARK 465 ALA D 2 REMARK 465 GLU D 3 REMARK 465 ALA D 4 REMARK 465 ALA D 5 REMARK 465 SER D 6 REMARK 465 CYS D 7 REMARK 465 ALA D 8 REMARK 465 ARG D 9 REMARK 465 LYS D 10 REMARK 465 GLY D 11 REMARK 465 LEU D 211 REMARK 465 GLU D 212 REMARK 465 ASN D 213 REMARK 465 ILE D 214 REMARK 465 GLY D 215 REMARK 465 THR D 216 REMARK 465 GLU D 217 REMARK 465 TYR D 218 REMARK 465 GLN D 219 REMARK 465 ARG D 220 REMARK 465 SER D 221 REMARK 465 GLU D 222 REMARK 465 SER D 223 REMARK 465 SER D 224 REMARK 465 ILE D 225 REMARK 465 PHE D 226 REMARK 465 ASP D 227 REMARK 465 ALA D 228 REMARK 465 ILE D 229 REMARK 465 SER D 230 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LEU A 209 CG LEU A 209 CD1 -0.275 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 ALA A 15 -1.11 71.62 REMARK 500 ASN A 59 88.73 -157.85 REMARK 500 ARG A 105 -168.59 62.65 REMARK 500 ARG B 105 -169.75 63.76 REMARK 500 ALA C 15 -7.22 72.11 REMARK 500 GLU C 52 62.29 38.36 REMARK 500 ASN C 59 81.11 -150.44 REMARK 500 ASN C 61 46.95 38.65 REMARK 500 ARG C 105 -167.88 54.44 REMARK 500 SER C 199 8.46 127.70 REMARK 500 ALA D 15 -1.87 80.74 REMARK 500 ASN D 59 89.32 -153.44 REMARK 500 ASN D 61 29.46 44.71 REMARK 500 ARG D 105 -175.16 63.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR A 51 GLU A 52 -57.82 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 A2010 DISTANCE = 7.24 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCP D1211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCP C1209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCP B1210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCP A1210 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VP0 RELATED DB: PDB REMARK 900 STRUCTURAL STUDIES OF NUCLEOSIDE ANALOG AND FEEDBACK INHIBITOR REMARK 900 BINDING TO DROSOPHILA MELANOGASTER MULTISUBSTRATE REMARK 900 DEOXYRIBONUCLEOSIDE KINASE REMARK 900 RELATED ID: 2VP2 RELATED DB: PDB REMARK 900 STRUCTURAL STUDIES OF NUCLEOSIDE ANALOG AND FEEDBACK INHIBITOR REMARK 900 BINDING TO DROSOPHILA MELANOGASTER MULTISUBSTRATE REMARK 900 DEOXYRIBONUCLEOSIDE KINASE 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 2VP4 A 1 230 UNP Q9XZT6 DNK_DROME 1 230 DBREF 2VP4 B 1 230 UNP Q9XZT6 DNK_DROME 1 230 DBREF 2VP4 C 1 230 UNP Q9XZT6 DNK_DROME 1 230 DBREF 2VP4 D 1 230 UNP Q9XZT6 DNK_DROME 1 230 SEQRES 1 A 230 MET ALA GLU ALA ALA SER CYS ALA ARG LYS GLY THR LYS SEQRES 2 A 230 TYR ALA GLU GLY THR GLN PRO PHE THR VAL LEU ILE GLU SEQRES 3 A 230 GLY ASN ILE GLY SER GLY LYS THR THR TYR LEU ASN HIS SEQRES 4 A 230 PHE GLU LYS TYR LYS ASN ASP ILE CYS LEU LEU THR GLU SEQRES 5 A 230 PRO VAL GLU LYS TRP ARG ASN VAL ASN GLY VAL ASN LEU SEQRES 6 A 230 LEU GLU LEU MET TYR LYS ASP PRO LYS LYS TRP ALA MET SEQRES 7 A 230 PRO PHE GLN SER TYR VAL THR LEU THR MET LEU GLN SER SEQRES 8 A 230 HIS THR ALA PRO THR ASN LYS LYS LEU LYS ILE MET GLU SEQRES 9 A 230 ARG SER ILE PHE SER ALA ARG TYR CYS PHE VAL GLU ASN SEQRES 10 A 230 MET ARG ARG ASN GLY SER LEU GLU GLN GLY MET TYR ASN SEQRES 11 A 230 THR LEU GLU GLU TRP TYR LYS PHE ILE GLU GLU SER ILE SEQRES 12 A 230 HIS VAL GLN ALA ASP LEU ILE ILE TYR LEU ARG THR SER SEQRES 13 A 230 PRO GLU VAL ALA TYR GLU ARG ILE ARG GLN ARG ALA ARG SEQRES 14 A 230 SER GLU GLU SER CYS VAL PRO LEU LYS TYR LEU GLN GLU SEQRES 15 A 230 LEU HIS GLU LEU HIS GLU ASP TRP LEU ILE HIS GLN ARG SEQRES 16 A 230 ARG PRO GLN SER CYS LYS VAL LEU VAL LEU ASP ALA ASP SEQRES 17 A 230 LEU ASN LEU GLU ASN ILE GLY THR GLU TYR GLN ARG SER SEQRES 18 A 230 GLU SER SER ILE PHE ASP ALA ILE SER SEQRES 1 B 230 MET ALA GLU ALA ALA SER CYS ALA ARG LYS GLY THR LYS SEQRES 2 B 230 TYR ALA GLU GLY THR GLN PRO PHE THR VAL LEU ILE GLU SEQRES 3 B 230 GLY ASN ILE GLY SER GLY LYS THR THR TYR LEU ASN HIS SEQRES 4 B 230 PHE GLU LYS TYR LYS ASN ASP ILE CYS LEU LEU THR GLU SEQRES 5 B 230 PRO VAL GLU LYS TRP ARG ASN VAL ASN GLY VAL ASN LEU SEQRES 6 B 230 LEU GLU LEU MET TYR LYS ASP PRO LYS LYS TRP ALA MET SEQRES 7 B 230 PRO PHE GLN SER TYR VAL THR LEU THR MET LEU GLN SER SEQRES 8 B 230 HIS THR ALA PRO THR ASN LYS LYS LEU LYS ILE MET GLU SEQRES 9 B 230 ARG SER ILE PHE SER ALA ARG TYR CYS PHE VAL GLU ASN SEQRES 10 B 230 MET ARG ARG ASN GLY SER LEU GLU GLN GLY MET TYR ASN SEQRES 11 B 230 THR LEU GLU GLU TRP TYR LYS PHE ILE GLU GLU SER ILE SEQRES 12 B 230 HIS VAL GLN ALA ASP LEU ILE ILE TYR LEU ARG THR SER SEQRES 13 B 230 PRO GLU VAL ALA TYR GLU ARG ILE ARG GLN ARG ALA ARG SEQRES 14 B 230 SER GLU GLU SER CYS VAL PRO LEU LYS TYR LEU GLN GLU SEQRES 15 B 230 LEU HIS GLU LEU HIS GLU ASP TRP LEU ILE HIS GLN ARG SEQRES 16 B 230 ARG PRO GLN SER CYS LYS VAL LEU VAL LEU ASP ALA ASP SEQRES 17 B 230 LEU ASN LEU GLU ASN ILE GLY THR GLU TYR GLN ARG SER SEQRES 18 B 230 GLU SER SER ILE PHE ASP ALA ILE SER SEQRES 1 C 230 MET ALA GLU ALA ALA SER CYS ALA ARG LYS GLY THR LYS SEQRES 2 C 230 TYR ALA GLU GLY THR GLN PRO PHE THR VAL LEU ILE GLU SEQRES 3 C 230 GLY ASN ILE GLY SER GLY LYS THR THR TYR LEU ASN HIS SEQRES 4 C 230 PHE GLU LYS TYR LYS ASN ASP ILE CYS LEU LEU THR GLU SEQRES 5 C 230 PRO VAL GLU LYS TRP ARG ASN VAL ASN GLY VAL ASN LEU SEQRES 6 C 230 LEU GLU LEU MET TYR LYS ASP PRO LYS LYS TRP ALA MET SEQRES 7 C 230 PRO PHE GLN SER TYR VAL THR LEU THR MET LEU GLN SER SEQRES 8 C 230 HIS THR ALA PRO THR ASN LYS LYS LEU LYS ILE MET GLU SEQRES 9 C 230 ARG SER ILE PHE SER ALA ARG TYR CYS PHE VAL GLU ASN SEQRES 10 C 230 MET ARG ARG ASN GLY SER LEU GLU GLN GLY MET TYR ASN SEQRES 11 C 230 THR LEU GLU GLU TRP TYR LYS PHE ILE GLU GLU SER ILE SEQRES 12 C 230 HIS VAL GLN ALA ASP LEU ILE ILE TYR LEU ARG THR SER SEQRES 13 C 230 PRO GLU VAL ALA TYR GLU ARG ILE ARG GLN ARG ALA ARG SEQRES 14 C 230 SER GLU GLU SER CYS VAL PRO LEU LYS TYR LEU GLN GLU SEQRES 15 C 230 LEU HIS GLU LEU HIS GLU ASP TRP LEU ILE HIS GLN ARG SEQRES 16 C 230 ARG PRO GLN SER CYS LYS VAL LEU VAL LEU ASP ALA ASP SEQRES 17 C 230 LEU ASN LEU GLU ASN ILE GLY THR GLU TYR GLN ARG SER SEQRES 18 C 230 GLU SER SER ILE PHE ASP ALA ILE SER SEQRES 1 D 230 MET ALA GLU ALA ALA SER CYS ALA ARG LYS GLY THR LYS SEQRES 2 D 230 TYR ALA GLU GLY THR GLN PRO PHE THR VAL LEU ILE GLU SEQRES 3 D 230 GLY ASN ILE GLY SER GLY LYS THR THR TYR LEU ASN HIS SEQRES 4 D 230 PHE GLU LYS TYR LYS ASN ASP ILE CYS LEU LEU THR GLU SEQRES 5 D 230 PRO VAL GLU LYS TRP ARG ASN VAL ASN GLY VAL ASN LEU SEQRES 6 D 230 LEU GLU LEU MET TYR LYS ASP PRO LYS LYS TRP ALA MET SEQRES 7 D 230 PRO PHE GLN SER TYR VAL THR LEU THR MET LEU GLN SER SEQRES 8 D 230 HIS THR ALA PRO THR ASN LYS LYS LEU LYS ILE MET GLU SEQRES 9 D 230 ARG SER ILE PHE SER ALA ARG TYR CYS PHE VAL GLU ASN SEQRES 10 D 230 MET ARG ARG ASN GLY SER LEU GLU GLN GLY MET TYR ASN SEQRES 11 D 230 THR LEU GLU GLU TRP TYR LYS PHE ILE GLU GLU SER ILE SEQRES 12 D 230 HIS VAL GLN ALA ASP LEU ILE ILE TYR LEU ARG THR SER SEQRES 13 D 230 PRO GLU VAL ALA TYR GLU ARG ILE ARG GLN ARG ALA ARG SEQRES 14 D 230 SER GLU GLU SER CYS VAL PRO LEU LYS TYR LEU GLN GLU SEQRES 15 D 230 LEU HIS GLU LEU HIS GLU ASP TRP LEU ILE HIS GLN ARG SEQRES 16 D 230 ARG PRO GLN SER CYS LYS VAL LEU VAL LEU ASP ALA ASP SEQRES 17 D 230 LEU ASN LEU GLU ASN ILE GLY THR GLU TYR GLN ARG SER SEQRES 18 D 230 GLU SER SER ILE PHE ASP ALA ILE SER HET DCP A1210 28 HET DCP B1210 28 HET DCP C1209 28 HET DCP D1211 28 HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE FORMUL 5 DCP 4(C9 H16 N3 O13 P3) FORMUL 9 HOH *459(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 ALA A 94 1 23 HELIX 6 6 SER A 106 CYS A 113 1 8 HELIX 7 7 CYS A 113 GLY A 122 1 10 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 GLY B 122 1 10 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 HELIX 23 23 GLY C 32 HIS C 39 1 8 HELIX 24 24 PHE C 40 LYS C 44 5 5 HELIX 25 25 PRO C 53 ARG C 58 1 6 HELIX 26 26 ASN C 64 ASP C 72 1 9 HELIX 27 27 ASP C 72 ALA C 94 1 23 HELIX 28 28 SER C 106 CYS C 113 1 8 HELIX 29 29 CYS C 113 ASN C 121 1 9 HELIX 30 30 GLU C 125 ILE C 143 1 19 HELIX 31 31 SER C 156 ALA C 168 1 13 HELIX 32 32 ARG C 169 SER C 173 5 5 HELIX 33 33 PRO C 176 ILE C 192 1 17 HELIX 34 34 GLY D 32 HIS D 39 1 8 HELIX 35 35 PHE D 40 LYS D 44 5 5 HELIX 36 36 PRO D 53 ARG D 58 1 6 HELIX 37 37 ASN D 64 ASP D 72 1 9 HELIX 38 38 ASP D 72 ALA D 94 1 23 HELIX 39 39 SER D 106 CYS D 113 1 8 HELIX 40 40 CYS D 113 ASN D 121 1 9 HELIX 41 41 GLU D 125 ILE D 143 1 19 HELIX 42 42 SER D 156 ALA D 168 1 13 HELIX 43 43 ARG D 169 SER D 173 5 5 HELIX 44 44 PRO D 176 ILE D 192 1 17 SHEET 1 AA 5 ILE A 47 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 SHEET 1 CA 5 ILE C 47 LEU C 50 0 SHEET 2 CA 5 LEU C 100 GLU C 104 1 O LEU C 100 N CYS C 48 SHEET 3 CA 5 PHE C 21 GLU C 26 1 O PHE C 21 N LYS C 101 SHEET 4 CA 5 LEU C 149 ARG C 154 1 O LEU C 149 N LEU C 24 SHEET 5 CA 5 LYS C 201 ASP C 206 1 O LYS C 201 N ILE C 150 SHEET 1 DA 5 ILE D 47 LEU D 50 0 SHEET 2 DA 5 LEU D 100 GLU D 104 1 O LEU D 100 N CYS D 48 SHEET 3 DA 5 PHE D 21 GLU D 26 1 O PHE D 21 N LYS D 101 SHEET 4 DA 5 LEU D 149 ARG D 154 1 O LEU D 149 N LEU D 24 SHEET 5 DA 5 LYS D 201 ASP D 206 1 O LYS D 201 N ILE D 150 CISPEP 1 GLN C 198 SER C 199 0 -5.93 SITE 1 AC1 25 ILE D 29 GLY D 30 SER D 31 GLY D 32 SITE 2 AC1 25 LYS D 33 THR D 34 TRP D 57 LEU D 66 SITE 3 AC1 25 MET D 69 TYR D 70 PHE D 80 GLN D 81 SITE 4 AC1 25 VAL D 84 GLU D 104 ARG D 105 ALA D 110 SITE 5 AC1 25 PHE D 114 MET D 118 ARG D 167 ARG D 169 SITE 6 AC1 25 GLU D 172 HOH D2085 HOH D2103 HOH D2104 SITE 7 AC1 25 HOH D2105 SITE 1 AC2 25 ILE C 29 GLY C 30 SER C 31 GLY C 32 SITE 2 AC2 25 LYS C 33 THR C 34 TRP C 57 LEU C 66 SITE 3 AC2 25 MET C 69 TYR C 70 PHE C 80 GLN C 81 SITE 4 AC2 25 VAL C 84 GLU C 104 ARG C 105 ALA C 110 SITE 5 AC2 25 PHE C 114 MET C 118 ARG C 167 ARG C 169 SITE 6 AC2 25 GLU C 172 HOH C2089 HOH C2104 HOH C2105 SITE 7 AC2 25 HOH C2106 SITE 1 AC3 23 ILE B 29 GLY B 30 SER B 31 GLY B 32 SITE 2 AC3 23 LYS B 33 THR B 34 VAL B 54 TRP B 57 SITE 3 AC3 23 TYR B 70 PHE B 80 GLN B 81 VAL B 84 SITE 4 AC3 23 GLU B 104 ARG B 105 ALA B 110 PHE B 114 SITE 5 AC3 23 ARG B 167 ARG B 169 GLU B 172 HOH B2099 SITE 6 AC3 23 HOH B2119 HOH B2120 HOH B2121 SITE 1 AC4 24 ILE A 29 GLY A 30 SER A 31 GLY A 32 SITE 2 AC4 24 LYS A 33 THR A 34 TRP A 57 LEU A 66 SITE 3 AC4 24 MET A 69 TYR A 70 PHE A 80 GLN A 81 SITE 4 AC4 24 VAL A 84 GLU A 104 ARG A 105 ALA A 110 SITE 5 AC4 24 PHE A 114 ARG A 167 ARG A 169 GLU A 172 SITE 6 AC4 24 HOH A2105 HOH A2125 HOH A2126 HOH A2127 CRYST1 67.858 119.034 70.511 90.00 96.38 90.00 P 1 21 1 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 0.014737 0.000000 0.001648 0.00000 SCALE2 0.000000 0.008401 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014271 0.00000 MTRIX1 1 -1.000000 -0.004896 0.005218 59.63000 1 MTRIX2 1 0.004766 -0.999700 -0.024640 1.22600 1 MTRIX3 1 0.005337 -0.024610 0.999700 -0.17690 1