HEADER TRANSFERASE/TRANSFERASE INHIBITOR 03-APR-14 4Q1B TITLE HUMAN DCK C4S-S74E MUTANT IN COMPLEX WITH UDP AND THE INHIBITOR 7 {N- TITLE 2 (2-(3-(4-(((4,6-DIAMINOPYRIMIDIN-2-YL)THIO)METHYL)-5-PROPYLTHIAZOL-2- TITLE 3 YL)PHENOXY)ETHYL)METHANESULFONAMIDE} 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 C41; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET14B KEYWDS PHOSPHORYL TRANSFER, PHOSPHORYLATION, DEOXYCYTIDINE, TRANSFERASE, KEYWDS 2 INHIBITOR COMPLEX, KINASE, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.NOMME,A.LAVIE REVDAT 1 18-FEB-15 4Q1B 0 JRNL AUTH J.NOMME,Z.LI,R.M.GIPSON,J.WANG,A.L.ARMIJO,T.LE,S.PODDAR, JRNL AUTH 2 T.SMITH,B.D.SANTARSIERO,H.A.NGUYEN,J.CZERNIN, JRNL AUTH 3 A.N.ALEXANDROVA,M.E.JUNG,C.G.RADU,A.LAVIE JRNL TITL STRUCTURE-GUIDED DEVELOPMENT OF DEOXYCYTIDINE KINASE JRNL TITL 2 INHIBITORS WITH NANOMOLAR AFFINITY AND IMPROVED METABOLIC JRNL TITL 3 STABILITY. JRNL REF J.MED.CHEM. V. 57 9480 2014 JRNL REFN ISSN 0022-2623 JRNL PMID 25341194 JRNL DOI 10.1021/JM501124J REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 28349 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1540 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2074 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.2100 REMARK 3 BIN FREE R VALUE SET COUNT : 102 REMARK 3 BIN FREE R VALUE : 0.3710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3736 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 114 REMARK 3 SOLVENT ATOMS : 92 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.34000 REMARK 3 B22 (A**2) : -3.34000 REMARK 3 B33 (A**2) : 6.68000 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): 0.046 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.044 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.122 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.455 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3963 ; 0.012 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5391 ; 1.696 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 458 ; 7.238 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;39.478 ;24.219 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 660 ;19.917 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;16.522 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 577 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2998 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1829 ; 4.026 ; 5.453 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2279 ; 5.598 ; 8.164 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2134 ; 4.139 ; 5.396 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6268 ; 8.036 ;45.423 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 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.504 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : -H, K, -L REMARK 3 TWIN FRACTION : 0.496 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4Q1B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-14. REMARK 100 THE RCSB ID CODE IS RCSB085479. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-13 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 : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : C111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30472 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 17.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.55200 REMARK 200 FOR SHELL : 2.870 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: PDB ENTRY 4JLN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M TRISODIUM CITRATE DEHYDRATE AND REMARK 280 25 MM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 60.97200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.48600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 91.45800 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: 3800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 THR A 19 REMARK 465 ASN A 60 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 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 ASN B 60 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 GLY B 167 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 115 CG CD CE NZ REMARK 470 LYS A 117 CG CD CE NZ REMARK 470 GLU A 120 CG CD OE1 OE2 REMARK 470 GLU A 197 CG CD OE1 OE2 REMARK 470 GLN A 198 CG CD OE1 NE2 REMARK 470 ILE A 200 CG1 CG2 CD1 REMARK 470 LYS A 207 CG CD CE NZ REMARK 470 LYS A 222 CG CD CE NZ REMARK 470 GLN A 229 CG CD OE1 NE2 REMARK 470 GLU A 230 CG CD OE1 OE2 REMARK 470 GLU A 240 CG CD OE1 OE2 REMARK 470 LYS A 243 CG CD CE NZ REMARK 470 MET B 73 CG SD CE REMARK 470 GLU B 87 CG CD OE1 OE2 REMARK 470 LYS B 115 CG CD CE NZ REMARK 470 ASN B 164 CG OD1 ND2 REMARK 470 TYR B 190 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN B 195 CG OD1 ND2 REMARK 470 GLU B 203 CG CD OE1 OE2 REMARK 470 LYS B 222 CG CD CE NZ REMARK 470 ASP B 226 CG OD1 OD2 REMARK 470 GLN B 229 CG CD OE1 NE2 REMARK 470 GLU B 230 CG CD OE1 OE2 REMARK 470 LYS B 245 CG CD CE 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 OH TYR B 177 O HOH B 445 1.77 REMARK 500 O HIS A 209 O HOH A 430 1.80 REMARK 500 O TRP A 48 O HOH A 405 1.92 REMARK 500 OE1 GLN B 156 O HOH B 431 2.01 REMARK 500 OE1 GLU B 247 O HOH B 403 2.10 REMARK 500 O GLN B 97 O HOH B 401 2.11 REMARK 500 N GLU A 213 O HOH A 430 2.14 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 PRO A 54 C - N - CA ANGL. DEV. = 9.5 DEGREES REMARK 500 LEU B 202 CA - CB - CG ANGL. DEV. = 15.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 54 -60.52 -23.30 REMARK 500 LYS A 88 65.28 -158.20 REMARK 500 LYS A 115 175.82 -54.57 REMARK 500 ARG A 128 -171.20 62.48 REMARK 500 SER A 169 28.54 -71.08 REMARK 500 ILE A 200 123.23 -35.44 REMARK 500 PRO A 201 150.22 -48.19 REMARK 500 GLU A 203 -38.10 -35.00 REMARK 500 ASN A 224 22.55 -71.05 REMARK 500 ASP A 241 150.77 -46.79 REMARK 500 PHE A 242 -5.24 -146.81 REMARK 500 LYS A 243 -8.31 -53.79 REMARK 500 THR A 259 5.79 -61.83 REMARK 500 ILE B 30 133.92 -34.86 REMARK 500 LYS B 121 69.47 -116.40 REMARK 500 ARG B 128 169.30 58.89 REMARK 500 ILE B 136 -70.62 -115.33 REMARK 500 THR B 181 150.80 -41.13 REMARK 500 LEU B 217 -73.25 -102.16 REMARK 500 GLU B 230 13.91 -146.75 REMARK 500 VAL B 238 30.74 -97.30 REMARK 500 LYS B 245 100.76 -160.03 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 427 DISTANCE = 5.11 ANGSTROMS REMARK 525 HOH A 434 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH B 448 DISTANCE = 5.31 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2Y0 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2Y0 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP B 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Q18 RELATED DB: PDB REMARK 900 RELATED ID: 4Q19 RELATED DB: PDB REMARK 900 RELATED ID: 4Q1A RELATED DB: PDB REMARK 900 RELATED ID: 4Q1C RELATED DB: PDB REMARK 900 RELATED ID: 4Q1D RELATED DB: PDB REMARK 900 RELATED ID: 4Q1E RELATED DB: PDB REMARK 900 RELATED ID: 4Q1F RELATED DB: PDB DBREF 4Q1B A 1 260 UNP P27707 DCK_HUMAN 1 260 DBREF 4Q1B B 1 260 UNP P27707 DCK_HUMAN 1 260 SEQADV 4Q1B MET A -19 UNP P27707 EXPRESSION TAG SEQADV 4Q1B GLY A -18 UNP P27707 EXPRESSION TAG SEQADV 4Q1B SER A -17 UNP P27707 EXPRESSION TAG SEQADV 4Q1B SER A -16 UNP P27707 EXPRESSION TAG SEQADV 4Q1B HIS A -15 UNP P27707 EXPRESSION TAG SEQADV 4Q1B HIS A -14 UNP P27707 EXPRESSION TAG SEQADV 4Q1B HIS A -13 UNP P27707 EXPRESSION TAG SEQADV 4Q1B HIS A -12 UNP P27707 EXPRESSION TAG SEQADV 4Q1B HIS A -11 UNP P27707 EXPRESSION TAG SEQADV 4Q1B HIS A -10 UNP P27707 EXPRESSION TAG SEQADV 4Q1B SER A -9 UNP P27707 EXPRESSION TAG SEQADV 4Q1B SER A -8 UNP P27707 EXPRESSION TAG SEQADV 4Q1B GLY A -7 UNP P27707 EXPRESSION TAG SEQADV 4Q1B LEU A -6 UNP P27707 EXPRESSION TAG SEQADV 4Q1B VAL A -5 UNP P27707 EXPRESSION TAG SEQADV 4Q1B PRO A -4 UNP P27707 EXPRESSION TAG SEQADV 4Q1B ARG A -3 UNP P27707 EXPRESSION TAG SEQADV 4Q1B GLY A -2 UNP P27707 EXPRESSION TAG SEQADV 4Q1B SER A -1 UNP P27707 EXPRESSION TAG SEQADV 4Q1B HIS A 0 UNP P27707 EXPRESSION TAG SEQADV 4Q1B SER A 9 UNP P27707 CYS 9 ENGINEERED MUTATION SEQADV 4Q1B SER A 45 UNP P27707 CYS 45 ENGINEERED MUTATION SEQADV 4Q1B SER A 59 UNP P27707 CYS 59 ENGINEERED MUTATION SEQADV 4Q1B GLU A 74 UNP P27707 SER 74 ENGINEERED MUTATION SEQADV 4Q1B SER A 146 UNP P27707 CYS 146 ENGINEERED MUTATION SEQADV 4Q1B MET B -19 UNP P27707 EXPRESSION TAG SEQADV 4Q1B GLY B -18 UNP P27707 EXPRESSION TAG SEQADV 4Q1B SER B -17 UNP P27707 EXPRESSION TAG SEQADV 4Q1B SER B -16 UNP P27707 EXPRESSION TAG SEQADV 4Q1B HIS B -15 UNP P27707 EXPRESSION TAG SEQADV 4Q1B HIS B -14 UNP P27707 EXPRESSION TAG SEQADV 4Q1B HIS B -13 UNP P27707 EXPRESSION TAG SEQADV 4Q1B HIS B -12 UNP P27707 EXPRESSION TAG SEQADV 4Q1B HIS B -11 UNP P27707 EXPRESSION TAG SEQADV 4Q1B HIS B -10 UNP P27707 EXPRESSION TAG SEQADV 4Q1B SER B -9 UNP P27707 EXPRESSION TAG SEQADV 4Q1B SER B -8 UNP P27707 EXPRESSION TAG SEQADV 4Q1B GLY B -7 UNP P27707 EXPRESSION TAG SEQADV 4Q1B LEU B -6 UNP P27707 EXPRESSION TAG SEQADV 4Q1B VAL B -5 UNP P27707 EXPRESSION TAG SEQADV 4Q1B PRO B -4 UNP P27707 EXPRESSION TAG SEQADV 4Q1B ARG B -3 UNP P27707 EXPRESSION TAG SEQADV 4Q1B GLY B -2 UNP P27707 EXPRESSION TAG SEQADV 4Q1B SER B -1 UNP P27707 EXPRESSION TAG SEQADV 4Q1B HIS B 0 UNP P27707 EXPRESSION TAG SEQADV 4Q1B SER B 9 UNP P27707 CYS 9 ENGINEERED MUTATION SEQADV 4Q1B SER B 45 UNP P27707 CYS 45 ENGINEERED MUTATION SEQADV 4Q1B SER B 59 UNP P27707 CYS 59 ENGINEERED MUTATION SEQADV 4Q1B GLU B 74 UNP P27707 SER 74 ENGINEERED MUTATION SEQADV 4Q1B SER B 146 UNP P27707 CYS 146 ENGINEERED MUTATION SEQRES 1 A 280 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 280 LEU VAL PRO ARG GLY SER HIS MET ALA THR PRO PRO LYS SEQRES 3 A 280 ARG SER SER PRO SER PHE SER ALA SER SER GLU GLY THR SEQRES 4 A 280 ARG ILE LYS LYS ILE SER ILE GLU GLY ASN ILE ALA ALA SEQRES 5 A 280 GLY LYS SER THR PHE VAL ASN ILE LEU LYS GLN LEU SER SEQRES 6 A 280 GLU ASP TRP GLU VAL VAL PRO GLU PRO VAL ALA ARG TRP SEQRES 7 A 280 SER ASN VAL GLN SER THR GLN ASP GLU PHE GLU GLU LEU SEQRES 8 A 280 THR MET GLU 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 GLU 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 2Y0 A 301 32 HET UDP A 302 25 HET 2Y0 B 301 32 HET UDP B 302 25 HETNAM 2Y0 N-(2-(3-(4-(((4,6-DIAMINOPYRIMIDIN-2-YL)THIO)METHYL)-5- HETNAM 2 2Y0 PROPYLTHIAZOL-2-YL)PHENOXY)ETHYL)METHANESULFONAMIDE HETNAM UDP URIDINE-5'-DIPHOSPHATE HETSYN 2Y0 N-{2-[3-(4-{[(4,6-DIAMINOPYRIMIDIN-2-YL) HETSYN 2 2Y0 SULFANYL]METHYL}-5-PROPYL-1,3-THIAZOL-2-YL) HETSYN 3 2Y0 PHENOXY]ETHYL}METHANESULFONAMIDE FORMUL 3 2Y0 2(C20 H26 N6 O3 S3) FORMUL 4 UDP 2(C9 H14 N2 O12 P2) FORMUL 7 HOH *92(H2 O) HELIX 1 1 GLY A 33 LYS A 42 1 10 HELIX 2 2 GLU A 53 SER A 59 1 7 HELIX 3 3 MET A 73 LYS A 88 1 16 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 GLU A 183 ARG A 192 1 10 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 GLN A 229 5 5 HELIX 13 13 TYR A 246 THR A 259 1 14 HELIX 14 14 GLY B 33 GLN B 43 1 11 HELIX 15 15 GLU B 53 SER B 59 1 7 HELIX 16 16 MET B 73 LYS B 88 1 16 HELIX 17 17 LYS B 88 LYS B 115 1 28 HELIX 18 18 SER B 129 ILE B 136 1 8 HELIX 19 19 ILE B 136 SER B 144 1 9 HELIX 20 20 ASN B 148 PHE B 166 1 19 HELIX 21 21 THR B 181 TYR B 190 1 10 HELIX 22 22 PRO B 201 LEU B 217 1 17 HELIX 23 23 PHE B 225 GLU B 230 5 6 HELIX 24 24 TYR B 246 SER B 258 1 13 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 ILE A 24 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 234 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 VAL B 123 N GLU B 49 SHEET 3 B 5 LYS B 22 GLU B 27 1 N ILE B 26 O PHE B 126 SHEET 4 B 5 GLY B 174 GLN B 179 1 O LEU B 178 N GLU B 27 SHEET 5 B 5 ILE B 233 ASP B 237 1 O LEU B 236 N TYR B 177 SITE 1 AC1 14 GLU A 53 VAL A 55 LEU A 82 TYR A 86 SITE 2 AC1 14 GLN A 97 ARG A 128 ASP A 133 PHE A 137 SITE 3 AC1 14 ASN A 140 SER A 144 TYR A 204 LYS A 207 SITE 4 AC1 14 HOH A 406 HOH A 423 SITE 1 AC2 13 ASN A 29 ALA A 31 ALA A 32 GLY A 33 SITE 2 AC2 13 LYS A 34 SER A 35 THR A 36 GLU A 127 SITE 3 AC2 13 ARG A 188 ARG A 192 ASP A 241 PHE A 242 SITE 4 AC2 13 LYS A 243 SITE 1 AC3 13 ILE B 30 GLU B 53 VAL B 55 MET B 85 SITE 2 AC3 13 PHE B 96 GLN B 97 ARG B 128 ASP B 133 SITE 3 AC3 13 PHE B 137 LEU B 141 SER B 144 SER B 146 SITE 4 AC3 13 TYR B 204 SITE 1 AC4 11 ALA B 31 ALA B 32 GLY B 33 LYS B 34 SITE 2 AC4 11 SER B 35 THR B 36 ARG B 188 ARG B 192 SITE 3 AC4 11 ASP B 241 PHE B 242 HOH B 432 CRYST1 68.968 68.968 121.944 90.00 90.00 90.00 P 41 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 0.014499 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014499 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008200 0.00000 MASTER 505 0 4 24 10 0 15 6 0 0 0 44 END