HEADER TRANSFERASE/TRANSFERASE INHIBITOR 18-AUG-09 3IPY TITLE X-RAY STRUCTURE OF HUMAN DEOXYCYTIDINE KINASE IN COMPLEX WITH AN TITLE 2 INHIBITOR 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606 KEYWDS HUMAN DEOXYCYTIDINE KINASE, ATP-BINDING, KINASE, NUCLEOTIDE-BINDING, KEYWDS 2 TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.W.TARI,R.V.SWANSON,M.HUNTER,I.HOFFMAN,T.R.STOUCH,K.G.CARSON REVDAT 2 06-SEP-23 3IPY 1 REMARK REVDAT 1 18-AUG-10 3IPY 0 JRNL AUTH T.C.JESSOP,J.E.TARVER,M.CARLSEN,A.XU,J.P.HEALY, JRNL AUTH 2 A.HEIM-RIETHER,Q.FU,J.A.TAYLOR,D.J.AUGERI,M.SHEN,T.R.STOUCH, JRNL AUTH 3 R.V.SWANSON,L.W.TARI,M.HUNTER,I.HOFFMAN,P.E.KEYES,X.C.YU, JRNL AUTH 4 M.MIRANDA,Q.LIU,J.C.SWAFFIELD,S.DAVID KIMBALL,A.NOURALDEEN, JRNL AUTH 5 A.G.WILSON,A.M.FOUSHEE,K.JHAVER,R.FINCH,S.ANDERSON, JRNL AUTH 6 T.ORAVECZ,K.G.CARSON JRNL TITL LEAD OPTIMIZATION AND STRUCTURE-BASED DESIGN OF POTENT AND JRNL TITL 2 BIOAVAILABLE DEOXYCYTIDINE KINASE INHIBITORS. JRNL REF BIOORG.MED.CHEM.LETT. V. 19 6784 2009 JRNL REFN ISSN 0960-894X JRNL PMID 19836232 JRNL DOI 10.1016/J.BMCL.2009.09.081 REMARK 2 REMARK 2 RESOLUTION. 2.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 119.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 20090 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 : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1071 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) : 2.54 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.61 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1441 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 66 REMARK 3 BIN FREE R VALUE : 0.3780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3743 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 134 REMARK 3 SOLVENT ATOMS : 110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.50000 REMARK 3 B22 (A**2) : 1.22000 REMARK 3 B33 (A**2) : -2.72000 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): 0.543 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.320 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.223 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.258 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.891 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3949 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5339 ; 1.404 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 446 ; 5.813 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 198 ;42.038 ;24.444 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 665 ;17.233 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;17.436 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 535 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3069 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1831 ; 0.204 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2673 ; 0.311 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 220 ; 0.153 ; 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): 66 ; 0.284 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.220 ; 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): 2286 ; 0.675 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3603 ; 1.175 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1947 ; 1.222 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1736 ; 1.977 ; 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3IPY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054718. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NOIR-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20090 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.540 REMARK 200 RESOLUTION RANGE LOW (A) : 119.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1P60 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, 25% PEG 4000, 8% REMARK 280 ISOPROPANOL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-Z+1/2 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 37.27800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 119.54850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.21400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 119.54850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.27800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.21400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 37.27800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.21400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 119.54850 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.21400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.27800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 119.54850 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 VAL A 61 REMARK 465 GLN A 62 REMARK 465 SER A 63 REMARK 465 THR A 64 REMARK 465 GLN A 65 REMARK 465 ASP A 66 REMARK 465 GLU A 67 REMARK 465 PHE A 68 REMARK 465 GLU A 69 REMARK 465 GLU A 70 REMARK 465 LEU A 71 REMARK 465 THR A 72 REMARK 465 MET A 73 REMARK 465 SER A 74 REMARK 465 GLN A 75 REMARK 465 LYS A 76 REMARK 465 VAL B 61 REMARK 465 GLN B 62 REMARK 465 SER B 63 REMARK 465 THR B 64 REMARK 465 GLN B 65 REMARK 465 ASP B 66 REMARK 465 GLU B 67 REMARK 465 PHE B 68 REMARK 465 GLU B 69 REMARK 465 GLU B 70 REMARK 465 LEU B 71 REMARK 465 THR B 72 REMARK 465 MET B 73 REMARK 465 SER B 74 REMARK 465 GLN B 75 REMARK 465 LYS B 76 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 TRP A 58 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 58 CZ3 CH2 REMARK 470 ASN A 77 CB CG OD1 ND2 REMARK 470 TRP B 58 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B 58 CZ3 CH2 REMARK 470 ASN B 77 CB CG OD1 ND2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ILE A 21 CG2 REMARK 480 LYS A 22 CD CE NZ REMARK 480 ILE A 40 CG1 CD1 REMARK 480 LEU A 41 CD1 REMARK 480 VAL A 50 CG1 REMARK 480 ALA A 56 CB REMARK 480 ALA A 110 CB REMARK 480 MET A 162 CE REMARK 480 VAL A 231 CG2 REMARK 480 GLU A 240 CD OE1 OE2 REMARK 480 LYS A 252 NZ REMARK 480 GLU A 255 CG CD OE1 OE2 REMARK 480 ILE B 21 CG2 REMARK 480 LYS B 22 CD CE NZ REMARK 480 ILE B 40 CG1 CD1 REMARK 480 LEU B 41 CD1 REMARK 480 VAL B 50 CG1 REMARK 480 VAL B 51 CG2 REMARK 480 ALA B 56 CB REMARK 480 ARG B 57 NH2 REMARK 480 LYS B 88 CD CE NZ REMARK 480 ILE B 105 CD1 REMARK 480 ALA B 110 CB REMARK 480 LEU B 112 CD2 REMARK 480 THR B 153 CG2 REMARK 480 MET B 162 CE REMARK 480 ASN B 164 CG OD1 ND2 REMARK 480 VAL B 231 CG2 REMARK 480 LYS B 243 NZ REMARK 480 SER B 248 OG REMARK 480 LYS B 252 NZ 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 O4 MLT B 262 O HOH B 332 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 ILE A 21 CB ILE A 21 CG2 -0.392 REMARK 500 LYS A 22 CG LYS A 22 CD -0.304 REMARK 500 ILE A 40 CB ILE A 40 CG1 -0.277 REMARK 500 VAL A 50 CB VAL A 50 CG1 -0.130 REMARK 500 ALA A 56 CA ALA A 56 CB -0.245 REMARK 500 GLU A 240 CG GLU A 240 CD -0.415 REMARK 500 GLU A 255 CB GLU A 255 CG -0.275 REMARK 500 GLU A 255 CG GLU A 255 CD -0.106 REMARK 500 GLU A 255 CD GLU A 255 OE1 0.087 REMARK 500 ILE B 21 CB ILE B 21 CG2 -0.419 REMARK 500 LYS B 22 CG LYS B 22 CD -0.303 REMARK 500 VAL B 50 CB VAL B 50 CG1 -0.183 REMARK 500 VAL B 51 CB VAL B 51 CG2 -0.213 REMARK 500 ALA B 56 CA ALA B 56 CB -0.325 REMARK 500 ARG B 57 CZ ARG B 57 NH2 -0.522 REMARK 500 LYS B 88 CE LYS B 88 NZ 0.316 REMARK 500 LEU B 112 CG LEU B 112 CD2 0.244 REMARK 500 THR B 153 CB THR B 153 CG2 -0.224 REMARK 500 ASN B 164 CB ASN B 164 CG -0.340 REMARK 500 VAL B 231 CB VAL B 231 CG2 0.179 REMARK 500 LYS B 243 CE LYS B 243 NZ -0.244 REMARK 500 LYS B 252 CE LYS B 252 NZ -0.473 REMARK 500 REMARK 500 REMARK: NULL 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 ILE A 21 CA - CB - CG2 ANGL. DEV. = 15.5 DEGREES REMARK 500 LYS A 22 CB - CG - CD ANGL. DEV. = 16.9 DEGREES REMARK 500 ILE A 40 CG1 - CB - CG2 ANGL. DEV. = 22.7 DEGREES REMARK 500 LEU A 41 CB - CG - CD1 ANGL. DEV. = -16.7 DEGREES REMARK 500 ALA A 56 N - CA - CB ANGL. DEV. = 14.5 DEGREES REMARK 500 VAL A 231 CG1 - CB - CG2 ANGL. DEV. = -20.2 DEGREES REMARK 500 LYS A 252 CD - CE - NZ ANGL. DEV. = -15.5 DEGREES REMARK 500 GLU A 255 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 ILE B 21 CG1 - CB - CG2 ANGL. DEV. = 17.0 DEGREES REMARK 500 LYS B 22 CB - CG - CD ANGL. DEV. = 34.8 DEGREES REMARK 500 LYS B 22 CG - CD - CE ANGL. DEV. = -19.6 DEGREES REMARK 500 ILE B 40 CG1 - CB - CG2 ANGL. DEV. = 31.6 DEGREES REMARK 500 LEU B 41 CB - CG - CD1 ANGL. DEV. = -19.3 DEGREES REMARK 500 VAL B 50 CA - CB - CG1 ANGL. DEV. = -12.0 DEGREES REMARK 500 VAL B 51 CA - CB - CG2 ANGL. DEV. = 13.8 DEGREES REMARK 500 ARG B 57 NH1 - CZ - NH2 ANGL. DEV. = -16.4 DEGREES REMARK 500 ARG B 57 NE - CZ - NH2 ANGL. DEV. = 16.1 DEGREES REMARK 500 LEU B 112 CD1 - CG - CD2 ANGL. DEV. = -40.6 DEGREES REMARK 500 LEU B 112 CB - CG - CD2 ANGL. DEV. = -16.6 DEGREES REMARK 500 THR B 153 CA - CB - CG2 ANGL. DEV. = 10.9 DEGREES REMARK 500 ASN B 164 CA - CB - CG ANGL. DEV. = 20.5 DEGREES REMARK 500 ASN B 164 CB - CG - OD1 ANGL. DEV. = -16.5 DEGREES REMARK 500 LYS B 252 CD - CE - NZ ANGL. DEV. = -18.3 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 ALA A 31 11.07 57.15 REMARK 500 LEU A 44 -111.20 -77.92 REMARK 500 LYS A 88 87.48 -158.42 REMARK 500 LEU A 112 -74.34 -82.64 REMARK 500 LYS A 115 63.43 -66.43 REMARK 500 LYS A 117 -82.97 -65.90 REMARK 500 ASP A 118 -64.87 20.85 REMARK 500 ALA A 119 -175.63 -62.55 REMARK 500 ARG A 128 -171.62 60.79 REMARK 500 VAL A 231 122.61 -30.47 REMARK 500 LYS A 245 8.94 -153.44 REMARK 500 ASN B 113 49.48 -109.58 REMARK 500 LYS B 115 41.44 39.38 REMARK 500 LEU B 116 -17.63 -179.25 REMARK 500 LYS B 117 11.82 -54.02 REMARK 500 GLU B 120 -18.30 57.69 REMARK 500 LYS B 121 56.11 -143.01 REMARK 500 ARG B 128 -177.85 58.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLU A 255 0.08 SIDE CHAIN 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 MLT A 261 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B87 A 263 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B87 A 264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLT B 262 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B87 B 265 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B87 B 266 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IPX RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF HUMAN DEOXYCYTIDINE KINASE IN COMPLEX WITH ADP REMARK 900 AND AN INHIBITOR DBREF 3IPY A 20 260 UNP P27707 DCK_HUMAN 20 260 DBREF 3IPY B 20 260 UNP P27707 DCK_HUMAN 20 260 SEQRES 1 A 241 ARG ILE LYS LYS ILE SER ILE GLU GLY ASN ILE ALA ALA SEQRES 2 A 241 GLY LYS SER THR PHE VAL ASN ILE LEU LYS GLN LEU CYS SEQRES 3 A 241 GLU ASP TRP GLU VAL VAL PRO GLU PRO VAL ALA ARG TRP SEQRES 4 A 241 CYS ASN VAL GLN SER THR GLN ASP GLU PHE GLU GLU LEU SEQRES 5 A 241 THR MET SER GLN LYS ASN GLY GLY ASN VAL LEU GLN MET SEQRES 6 A 241 MET TYR GLU LYS PRO GLU ARG TRP SER PHE THR PHE GLN SEQRES 7 A 241 THR TYR ALA CYS LEU SER ARG ILE ARG ALA GLN LEU ALA SEQRES 8 A 241 SER LEU ASN GLY LYS LEU LYS ASP ALA GLU LYS PRO VAL SEQRES 9 A 241 LEU PHE PHE GLU ARG SER VAL TYR SER ASP ARG TYR ILE SEQRES 10 A 241 PHE ALA SER ASN LEU TYR GLU SER GLU CYS MET ASN GLU SEQRES 11 A 241 THR GLU TRP THR ILE TYR GLN ASP TRP HIS ASP TRP MET SEQRES 12 A 241 ASN ASN GLN PHE GLY GLN SER LEU GLU LEU ASP GLY ILE SEQRES 13 A 241 ILE TYR LEU GLN ALA THR PRO GLU THR CYS LEU HIS ARG SEQRES 14 A 241 ILE TYR LEU ARG GLY ARG ASN GLU GLU GLN GLY ILE PRO SEQRES 15 A 241 LEU GLU TYR LEU GLU LYS LEU HIS TYR LYS HIS GLU SER SEQRES 16 A 241 TRP LEU LEU HIS ARG THR LEU LYS THR ASN PHE ASP TYR SEQRES 17 A 241 LEU GLN GLU VAL PRO ILE LEU THR LEU ASP VAL ASN GLU SEQRES 18 A 241 ASP PHE LYS ASP LYS TYR GLU SER LEU VAL GLU LYS VAL SEQRES 19 A 241 LYS GLU PHE LEU SER THR LEU SEQRES 1 B 241 ARG ILE LYS LYS ILE SER ILE GLU GLY ASN ILE ALA ALA SEQRES 2 B 241 GLY LYS SER THR PHE VAL ASN ILE LEU LYS GLN LEU CYS SEQRES 3 B 241 GLU ASP TRP GLU VAL VAL PRO GLU PRO VAL ALA ARG TRP SEQRES 4 B 241 CYS ASN VAL GLN SER THR GLN ASP GLU PHE GLU GLU LEU SEQRES 5 B 241 THR MET SER GLN LYS ASN GLY GLY ASN VAL LEU GLN MET SEQRES 6 B 241 MET TYR GLU LYS PRO GLU ARG TRP SER PHE THR PHE GLN SEQRES 7 B 241 THR TYR ALA CYS LEU SER ARG ILE ARG ALA GLN LEU ALA SEQRES 8 B 241 SER LEU ASN GLY LYS LEU LYS ASP ALA GLU LYS PRO VAL SEQRES 9 B 241 LEU PHE PHE GLU ARG SER VAL TYR SER ASP ARG TYR ILE SEQRES 10 B 241 PHE ALA SER ASN LEU TYR GLU SER GLU CYS MET ASN GLU SEQRES 11 B 241 THR GLU TRP THR ILE TYR GLN ASP TRP HIS ASP TRP MET SEQRES 12 B 241 ASN ASN GLN PHE GLY GLN SER LEU GLU LEU ASP GLY ILE SEQRES 13 B 241 ILE TYR LEU GLN ALA THR PRO GLU THR CYS LEU HIS ARG SEQRES 14 B 241 ILE TYR LEU ARG GLY ARG ASN GLU GLU GLN GLY ILE PRO SEQRES 15 B 241 LEU GLU TYR LEU GLU LYS LEU HIS TYR LYS HIS GLU SER SEQRES 16 B 241 TRP LEU LEU HIS ARG THR LEU LYS THR ASN PHE ASP TYR SEQRES 17 B 241 LEU GLN GLU VAL PRO ILE LEU THR LEU ASP VAL ASN GLU SEQRES 18 B 241 ASP PHE LYS ASP LYS TYR GLU SER LEU VAL GLU LYS VAL SEQRES 19 B 241 LYS GLU PHE LEU SER THR LEU HET MLT A 261 9 HET B87 A 263 29 HET B87 A 264 29 HET MLT B 262 9 HET B87 B 265 29 HET B87 B 266 29 HETNAM MLT D-MALATE HETNAM B87 4-(1-BENZOTHIOPHEN-2-YL)-6-[4-(2-OXO-2-PYRROLIDIN-1- HETNAM 2 B87 YLETHYL)PIPERAZIN-1-YL]PYRIMIDINE HETSYN MLT (2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID FORMUL 3 MLT 2(C4 H6 O5) FORMUL 4 B87 4(C22 H25 N5 O S) FORMUL 9 HOH *110(H2 O) HELIX 1 1 GLY A 33 LYS A 42 1 10 HELIX 2 2 GLU A 53 CYS A 59 1 7 HELIX 3 3 ASN A 80 LYS A 88 1 9 HELIX 4 4 LYS A 88 GLY A 114 1 27 HELIX 5 5 SER A 129 ILE A 136 1 8 HELIX 6 6 ILE A 136 SER A 144 1 9 HELIX 7 7 ASN A 148 GLY A 167 1 20 HELIX 8 8 GLN A 168 GLU A 171 5 4 HELIX 9 9 THR A 181 GLY A 193 1 13 HELIX 10 10 ARG A 194 GLN A 198 5 5 HELIX 11 11 PRO A 201 LEU A 217 1 17 HELIX 12 12 PHE A 225 GLU A 230 5 6 HELIX 13 13 ASP A 241 ASP A 244 5 4 HELIX 14 14 LYS A 245 LEU A 260 1 16 HELIX 15 15 GLY B 33 LYS B 42 1 10 HELIX 16 16 GLU B 53 CYS B 59 1 7 HELIX 17 17 ASN B 77 GLY B 79 5 3 HELIX 18 18 ASN B 80 LYS B 88 1 9 HELIX 19 19 LYS B 88 LEU B 112 1 25 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 GLU B 230 5 6 HELIX 27 27 ASP B 241 ASP B 244 5 4 HELIX 28 28 LYS B 245 SER B 258 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 24 O PHE A 126 SHEET 4 A 5 GLY A 174 GLN A 179 1 O ILE A 176 N SER A 25 SHEET 5 A 5 ILE A 233 ASP A 237 1 O LEU A 236 N GLN A 179 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 GLY B 28 1 N ILE B 24 O PHE B 126 SHEET 4 B 5 GLY B 174 GLN B 179 1 O LEU B 178 N GLU B 27 SHEET 5 B 5 ILE B 233 ASP B 237 1 O LEU B 236 N GLN B 179 CISPEP 1 ASN A 77 GLY A 78 0 -3.71 CISPEP 2 GLY B 114 LYS B 115 0 16.20 CISPEP 3 ASP B 118 ALA B 119 0 4.33 SITE 1 AC1 10 ILE A 30 ALA A 31 LYS A 34 SER A 35 SITE 2 AC1 10 GLU A 127 ARG A 128 ARG A 192 ARG A 194 SITE 3 AC1 10 B87 A 263 HOH A 333 SITE 1 AC2 14 ILE A 30 GLU A 53 TYR A 86 PHE A 96 SITE 2 AC2 14 GLN A 97 ARG A 104 ASP A 133 GLU A 196 SITE 3 AC2 14 ILE A 200 PRO A 201 TYR A 204 MLT A 261 SITE 4 AC2 14 B87 A 264 HOH A 335 SITE 1 AC3 12 MET A 85 TYR A 86 GLU A 90 ASN A 140 SITE 2 AC3 12 LEU A 141 SER A 144 GLU A 145 CYS A 146 SITE 3 AC3 12 TYR A 204 B87 A 263 HOH A 284 HOH A 337 SITE 1 AC4 8 ILE B 30 ALA B 31 LYS B 34 ARG B 128 SITE 2 AC4 8 ARG B 192 ARG B 194 B87 B 265 HOH B 332 SITE 1 AC5 16 ILE B 30 GLU B 53 TYR B 86 PHE B 96 SITE 2 AC5 16 GLN B 97 ASP B 133 PHE B 137 GLU B 196 SITE 3 AC5 16 ILE B 200 PRO B 201 TYR B 204 MLT B 262 SITE 4 AC5 16 B87 B 266 HOH B 307 HOH B 334 HOH B 340 SITE 1 AC6 10 MET B 85 TYR B 86 PHE B 96 ASN B 140 SITE 2 AC6 10 LEU B 141 SER B 144 TYR B 204 B87 B 265 SITE 3 AC6 10 HOH B 342 HOH B 344 CRYST1 74.556 74.428 239.097 90.00 90.00 90.00 I 21 21 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 0.013413 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013436 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004182 0.00000