HEADER TRANSFERASE/TRANSFERASE INHIBITOR 03-APR-14 4Q18 TITLE HUMAN DCK C4S-S74E MUTANT IN COMPLEX WITH UDP AND THE INHIBITOR 4 [1- TITLE 2 [5-(4-{[(2,6-DIAMINOPYRIMIDIN-4-YL)SULFANYL]METHYL}-5-PROPYL-1,3- TITLE 3 THIAZOL-2-YL)-2-METHOXYPHENOXY]-2-METHYLPROPAN-2-OL] 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 3 20-SEP-23 4Q18 1 REMARK SEQADV REVDAT 2 17-DEC-14 4Q18 1 JRNL REVDAT 1 05-NOV-14 4Q18 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. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 36194 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1924 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2701 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE SET COUNT : 120 REMARK 3 BIN FREE R VALUE : 0.3400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3788 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 178 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.98000 REMARK 3 B22 (A**2) : -2.98000 REMARK 3 B33 (A**2) : 5.95000 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): 0.036 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.031 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.468 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4110 ; 0.012 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3796 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5597 ; 1.656 ; 1.995 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8707 ; 1.105 ; 3.011 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 469 ; 6.295 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 199 ;41.649 ;24.422 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 687 ;16.813 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;17.484 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 585 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4572 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 985 ; 0.001 ; 0.020 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): 1852 ; 3.007 ; 4.638 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1851 ; 3.006 ; 4.638 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2311 ; 4.109 ; 6.940 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2312 ; 4.109 ; 6.940 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2258 ; 2.748 ; 4.717 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2259 ; 2.747 ; 4.717 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3281 ; 3.885 ; 7.040 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4952 ; 5.714 ;37.280 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4937 ; 5.707 ;37.267 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4Q18 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000085476. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-12 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 : 38119 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05900 REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.54700 REMARK 200 FOR SHELL : 2.750 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 (%): 44.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 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 61.22500 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 30.61250 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 91.83750 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: 20330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 ARG A 20 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 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 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 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 LEU A 71 CG CD1 CD2 REMARK 470 THR A 72 OG1 CG2 REMARK 470 LYS A 117 CG CD CE NZ REMARK 470 ASP A 118 CG OD1 OD2 REMARK 470 LYS A 222 CG CD CE NZ REMARK 470 GLU A 240 CG CD OE1 OE2 REMARK 470 THR B 19 OG1 CG2 REMARK 470 LEU B 71 CG CD1 CD2 REMARK 470 LYS B 76 CG CD CE NZ REMARK 470 LYS B 115 CG CD CE NZ REMARK 470 LYS B 117 CG CD CE NZ REMARK 470 GLU B 120 CG CD OE1 OE2 REMARK 470 ASN B 164 CG OD1 ND2 REMARK 470 TYR B 190 CG CD1 CD2 CE1 CE2 CZ OH 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 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 LYS B 42 O HOH B 534 2.06 REMARK 500 O TRP B 48 O HOH B 534 2.13 REMARK 500 OE2 GLU A 151 O HOH A 404 2.14 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 O HOH A 444 O HOH B 541 3455 1.61 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 ARG A 106 NE - CZ - NH1 ANGL. DEV. = 3.2 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 ARG A 128 -179.93 61.58 REMARK 500 SER A 169 -5.10 -52.58 REMARK 500 GLU A 171 135.66 -36.45 REMARK 500 THR A 181 153.25 -44.41 REMARK 500 LEU A 217 -73.47 -86.67 REMARK 500 LYS A 245 66.91 -156.85 REMARK 500 THR A 259 -5.67 -56.68 REMARK 500 THR B 72 177.25 -55.79 REMARK 500 LYS B 88 81.65 -163.95 REMARK 500 ARG B 128 179.06 73.04 REMARK 500 ILE B 136 -70.75 -91.08 REMARK 500 GLN B 168 -7.99 87.52 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 2XJ A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2XJ A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2XJ B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2XJ B 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Q19 RELATED DB: PDB REMARK 900 RELATED ID: 4Q1A RELATED DB: PDB REMARK 900 RELATED ID: 4Q1B 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 4Q18 A 1 260 UNP P27707 DCK_HUMAN 1 260 DBREF 4Q18 B 1 260 UNP P27707 DCK_HUMAN 1 260 SEQADV 4Q18 MET A -19 UNP P27707 EXPRESSION TAG SEQADV 4Q18 GLY A -18 UNP P27707 EXPRESSION TAG SEQADV 4Q18 SER A -17 UNP P27707 EXPRESSION TAG SEQADV 4Q18 SER A -16 UNP P27707 EXPRESSION TAG SEQADV 4Q18 HIS A -15 UNP P27707 EXPRESSION TAG SEQADV 4Q18 HIS A -14 UNP P27707 EXPRESSION TAG SEQADV 4Q18 HIS A -13 UNP P27707 EXPRESSION TAG SEQADV 4Q18 HIS A -12 UNP P27707 EXPRESSION TAG SEQADV 4Q18 HIS A -11 UNP P27707 EXPRESSION TAG SEQADV 4Q18 HIS A -10 UNP P27707 EXPRESSION TAG SEQADV 4Q18 SER A -9 UNP P27707 EXPRESSION TAG SEQADV 4Q18 SER A -8 UNP P27707 EXPRESSION TAG SEQADV 4Q18 GLY A -7 UNP P27707 EXPRESSION TAG SEQADV 4Q18 LEU A -6 UNP P27707 EXPRESSION TAG SEQADV 4Q18 VAL A -5 UNP P27707 EXPRESSION TAG SEQADV 4Q18 PRO A -4 UNP P27707 EXPRESSION TAG SEQADV 4Q18 ARG A -3 UNP P27707 EXPRESSION TAG SEQADV 4Q18 GLY A -2 UNP P27707 EXPRESSION TAG SEQADV 4Q18 SER A -1 UNP P27707 EXPRESSION TAG SEQADV 4Q18 HIS A 0 UNP P27707 EXPRESSION TAG SEQADV 4Q18 SER A 9 UNP P27707 CYS 9 ENGINEERED MUTATION SEQADV 4Q18 SER A 45 UNP P27707 CYS 45 ENGINEERED MUTATION SEQADV 4Q18 SER A 59 UNP P27707 CYS 59 ENGINEERED MUTATION SEQADV 4Q18 GLU A 74 UNP P27707 SER 74 ENGINEERED MUTATION SEQADV 4Q18 SER A 146 UNP P27707 CYS 146 ENGINEERED MUTATION SEQADV 4Q18 MET B -19 UNP P27707 EXPRESSION TAG SEQADV 4Q18 GLY B -18 UNP P27707 EXPRESSION TAG SEQADV 4Q18 SER B -17 UNP P27707 EXPRESSION TAG SEQADV 4Q18 SER B -16 UNP P27707 EXPRESSION TAG SEQADV 4Q18 HIS B -15 UNP P27707 EXPRESSION TAG SEQADV 4Q18 HIS B -14 UNP P27707 EXPRESSION TAG SEQADV 4Q18 HIS B -13 UNP P27707 EXPRESSION TAG SEQADV 4Q18 HIS B -12 UNP P27707 EXPRESSION TAG SEQADV 4Q18 HIS B -11 UNP P27707 EXPRESSION TAG SEQADV 4Q18 HIS B -10 UNP P27707 EXPRESSION TAG SEQADV 4Q18 SER B -9 UNP P27707 EXPRESSION TAG SEQADV 4Q18 SER B -8 UNP P27707 EXPRESSION TAG SEQADV 4Q18 GLY B -7 UNP P27707 EXPRESSION TAG SEQADV 4Q18 LEU B -6 UNP P27707 EXPRESSION TAG SEQADV 4Q18 VAL B -5 UNP P27707 EXPRESSION TAG SEQADV 4Q18 PRO B -4 UNP P27707 EXPRESSION TAG SEQADV 4Q18 ARG B -3 UNP P27707 EXPRESSION TAG SEQADV 4Q18 GLY B -2 UNP P27707 EXPRESSION TAG SEQADV 4Q18 SER B -1 UNP P27707 EXPRESSION TAG SEQADV 4Q18 HIS B 0 UNP P27707 EXPRESSION TAG SEQADV 4Q18 SER B 9 UNP P27707 CYS 9 ENGINEERED MUTATION SEQADV 4Q18 SER B 45 UNP P27707 CYS 45 ENGINEERED MUTATION SEQADV 4Q18 SER B 59 UNP P27707 CYS 59 ENGINEERED MUTATION SEQADV 4Q18 GLU B 74 UNP P27707 SER 74 ENGINEERED MUTATION SEQADV 4Q18 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 2XJ A 301 32 HET 2XJ A 302 32 HET UDP A 303 25 HET UDP B 401 25 HET 2XJ B 402 32 HET 2XJ B 403 32 HETNAM 2XJ 1-(5-(4-(((2,6-DIAMINOPYRIMIDIN-4-YL)THIO)METHYL)-5- HETNAM 2 2XJ PROPYLTHIAZOL-2-YL)-2-METHOXYPHENOXY)-2-METHYLPROPAN- HETNAM 3 2XJ 2-OL HETNAM UDP URIDINE-5'-DIPHOSPHATE HETSYN 2XJ 1-[5-(4-{[(2,6-DIAMINOPYRIMIDIN-4-YL)SULFANYL]METHYL}- HETSYN 2 2XJ 5-PROPYL-1,3-THIAZOL-2-YL)-2-METHOXYPHENOXY]-2- HETSYN 3 2XJ METHYLPROPAN-2-OL FORMUL 3 2XJ 4(C22 H29 N5 O3 S2) FORMUL 5 UDP 2(C9 H14 N2 O12 P2) FORMUL 9 HOH *88(H2 O) HELIX 1 1 GLY A 33 LYS A 42 1 10 HELIX 2 2 GLN A 43 SER A 45 5 3 HELIX 3 3 GLU A 53 SER A 59 1 7 HELIX 4 4 THR A 72 LYS A 88 1 17 HELIX 5 5 LYS A 88 GLY A 114 1 27 HELIX 6 6 SER A 129 ILE A 136 1 8 HELIX 7 7 ILE A 136 SER A 144 1 9 HELIX 8 8 ASN A 148 GLY A 167 1 20 HELIX 9 9 GLN A 168 GLU A 171 5 4 HELIX 10 10 THR A 181 GLY A 193 1 13 HELIX 11 11 ARG A 194 GLN A 198 5 5 HELIX 12 12 PRO A 201 LEU A 217 1 17 HELIX 13 13 PHE A 225 GLU A 230 5 6 HELIX 14 14 TYR A 246 THR A 259 1 14 HELIX 15 15 GLY B 33 SER B 45 1 13 HELIX 16 16 GLU B 53 SER B 59 1 7 HELIX 17 17 THR B 72 LYS B 88 1 17 HELIX 18 18 LYS B 88 LYS B 115 1 28 HELIX 19 19 SER B 129 ILE B 136 1 8 HELIX 20 20 ILE B 136 SER B 144 1 9 HELIX 21 21 ASN B 148 ASN B 164 1 17 HELIX 22 22 THR B 181 GLY B 193 1 13 HELIX 23 23 ARG B 194 GLY B 199 1 6 HELIX 24 24 PRO B 201 LEU B 217 1 17 HELIX 25 25 PHE B 225 VAL B 231 5 7 HELIX 26 26 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 26 O PHE A 126 SHEET 4 A 5 GLY A 174 GLN A 179 1 O ILE A 176 N GLU A 27 SHEET 5 A 5 ILE A 233 ASP A 237 1 O LEU A 236 N TYR A 177 SHEET 1 B 5 TRP B 48 VAL B 51 0 SHEET 2 B 5 VAL B 123 GLU B 127 1 O PHE B 125 N VAL B 51 SHEET 3 B 5 LYS B 22 GLU B 27 1 N LYS B 22 O LEU B 124 SHEET 4 B 5 GLY B 174 GLN B 179 1 O LEU B 178 N GLU B 27 SHEET 5 B 5 ILE B 233 ASP B 237 1 O LEU B 234 N ILE B 175 SITE 1 AC1 16 GLU A 53 VAL A 55 LEU A 82 TYR A 86 SITE 2 AC1 16 PRO A 89 PHE A 96 GLN A 97 ARG A 128 SITE 3 AC1 16 ASP A 133 PHE A 137 SER A 144 SER A 146 SITE 4 AC1 16 TYR A 204 2XJ A 302 HOH A 415 HOH A 424 SITE 1 AC2 9 ILE A 30 SER A 59 TYR A 86 GLU A 196 SITE 2 AC2 9 GLU A 197 GLY A 199 ILE A 200 TYR A 204 SITE 3 AC2 9 2XJ A 301 SITE 1 AC3 12 ALA A 31 ALA A 32 GLY A 33 LYS A 34 SITE 2 AC3 12 SER A 35 THR A 36 ARG A 188 ARG A 192 SITE 3 AC3 12 ASP A 241 PHE A 242 LYS A 243 HOH A 429 SITE 1 AC4 12 ALA B 31 ALA B 32 GLY B 33 LYS B 34 SITE 2 AC4 12 SER B 35 THR B 36 ARG B 188 ARG B 192 SITE 3 AC4 12 ASP B 241 PHE B 242 LYS B 243 HOH B 531 SITE 1 AC5 17 GLU B 53 VAL B 55 LEU B 82 MET B 85 SITE 2 AC5 17 TYR B 86 PRO B 89 PHE B 96 GLN B 97 SITE 3 AC5 17 ARG B 128 ASP B 133 PHE B 137 ASN B 140 SITE 4 AC5 17 LEU B 141 SER B 144 TYR B 204 LYS B 207 SITE 5 AC5 17 2XJ B 403 SITE 1 AC6 11 ILE B 30 SER B 59 TYR B 86 ARG B 194 SITE 2 AC6 11 GLU B 196 GLU B 197 GLY B 199 ILE B 200 SITE 3 AC6 11 PRO B 201 TYR B 204 2XJ B 402 CRYST1 68.750 68.750 122.450 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 0.014545 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014545 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008167 0.00000