HEADER TRANSFERASE 31-JAN-16 5FUW TITLE CATALYTIC DOMAIN OF THYMIDINE KINASE FROM TRYPANOSOMA BRUCEI WITH DTMP TITLE 2 OR DTHD COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMDINE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 EC: 2.7.1.21; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 3 ORGANISM_TAXID: 5691; SOURCE 4 VARIANT: LISTER427; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: 11347 KEYWDS TRANSFERASE, THYMIDINE KINASE, T.BRUCEI, TBTK, TKII, DTHD, DTMP EXPDTA X-RAY DIFFRACTION AUTHOR J.TIMM,M.VALENTE,V.CASTILLO-ACOSTA,T.BALZARINI,J.E.NETTLESHIP,H.RADA, AUTHOR 2 K.S.WILSON,D.GONZALEZ-PACANOWSKA REVDAT 3 10-JAN-24 5FUW 1 REMARK LINK REVDAT 2 09-NOV-16 5FUW 1 JRNL REVDAT 1 27-JUL-16 5FUW 0 JRNL AUTH M.VALENTE,J.TIMM,V.M.CASTILLO-ACOSTA,L.M.RUIZ-PEREZ, JRNL AUTH 2 T.BALZARINI,J.E.NETTLESHIP,L.E.BIRD,H.RADA,K.S.WILSON, JRNL AUTH 3 D.GONZALEZ-PACANOWSKA JRNL TITL CELL CYCLE REGULATION AND NOVEL STRUCTURAL FEATURES OF JRNL TITL 2 THYMIDINE KINASE, AN ESSENTIAL ENZYME IN TRYPANOSOMA BRUCEI. JRNL REF MOL.MICROBIOL. V. 102 365 2016 JRNL REFN ISSN 0950-382X JRNL PMID 27426054 JRNL DOI 10.1111/MMI.13467 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 115.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 34470 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1757 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) : 2498 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE SET COUNT : 151 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2577 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.23000 REMARK 3 B22 (A**2) : -1.23000 REMARK 3 B33 (A**2) : 2.45000 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): 0.144 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.128 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.101 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.160 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2692 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2512 ; 0.009 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3635 ; 2.160 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5748 ; 1.636 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 333 ; 6.675 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 117 ;35.005 ;22.735 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 454 ;12.572 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;11.105 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 408 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2994 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 620 ; 0.008 ; 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): 1338 ; 5.710 ; 5.354 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1337 ; 5.706 ; 5.351 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1666 ; 7.817 ; 7.993 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1667 ; 7.815 ; 7.997 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1354 ; 7.574 ; 5.905 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1338 ; 7.409 ; 5.891 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1945 ;10.463 ; 8.635 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 11349 ;12.472 ;51.445 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 11350 ;12.472 ;51.445 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 204 383 B 204 383 18368 0.12 0.05 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 5FUW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1290066161. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36299 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 64.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.60 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 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) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.80 REMARK 200 R MERGE FOR SHELL (I) : 0.88000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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 5FUV REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.0, 0.8 M SUCCINIC REMARK 280 ACID 1 MM TMP, 1 MM APPNHP, 3 MM MGCL2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 2 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+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -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 52.38500 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 78.57750 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 26.19250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.38500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 26.19250 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 78.57750 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.9 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2016 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2013 LIES ON A SPECIAL POSITION. 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 ARG A 246 REMARK 465 TYR A 247 REMARK 465 SER A 248 REMARK 465 GLU A 249 REMARK 465 GLY A 250 REMARK 465 ALA A 251 REMARK 465 ILE A 252 REMARK 465 THR A 253 REMARK 465 SER A 254 REMARK 465 HIS A 255 REMARK 465 ASP A 256 REMARK 465 GLN A 257 REMARK 465 ARG A 258 REMARK 465 ALA A 259 REMARK 465 ALA B 203 REMARK 465 ASP B 244 REMARK 465 THR B 245 REMARK 465 ARG B 246 REMARK 465 TYR B 247 REMARK 465 SER B 248 REMARK 465 GLU B 249 REMARK 465 GLY B 250 REMARK 465 ALA B 251 REMARK 465 ILE B 252 REMARK 465 THR B 253 REMARK 465 SER B 254 REMARK 465 HIS B 255 REMARK 465 ASP B 256 REMARK 465 GLN B 257 REMARK 465 ARG B 258 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 240 CE NZ REMARK 470 LEU A 260 CG CD1 CD2 REMARK 470 LYS A 357 CG CD CE NZ REMARK 470 ASN A 383 CG OD1 ND2 REMARK 470 MET A 384 CG SD CE REMARK 470 HIS B 204 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 275 CG CD OE1 OE2 REMARK 470 LYS B 278 CG CD CE NZ REMARK 470 ASP B 292 CG OD1 OD2 REMARK 470 GLU B 322 CG CD OE1 OE2 REMARK 470 LYS B 348 CG CD CE NZ REMARK 470 LYS B 357 CG CD CE NZ REMARK 470 MET B 384 CG SD CE 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 O1 PO4 B 1385 O HOH B 2009 2.09 REMARK 500 OD2 ASP A 271 O HOH A 2032 2.11 REMARK 500 O2 PO4 B 1385 O HOH B 2040 2.11 REMARK 500 O4 PO4 B 1385 O HOH B 2003 2.14 REMARK 500 OH TYR B 316 O HOH B 2027 2.14 REMARK 500 O1 PO4 A 1387 O HOH A 2006 2.19 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 224 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 228 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP A 315 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 330 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 330 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 224 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 330 NE - CZ - NH1 ANGL. DEV. = 3.5 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 SER A 358 156.33 176.92 REMARK 500 ALA B 262 134.86 -176.91 REMARK 500 SER B 358 160.57 174.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1389 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 341 SG REMARK 620 2 CYS A 344 SG 105.7 REMARK 620 3 CYS A 374 SG 113.7 121.8 REMARK 620 4 CYS A 377 SG 103.1 111.9 99.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1387 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 341 SG REMARK 620 2 CYS B 344 SG 106.2 REMARK 620 3 CYS B 374 SG 112.6 118.7 REMARK 620 4 CYS B 377 SG 107.7 113.6 97.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE QBT A 1386 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1387 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 1385 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1388 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THM B 1386 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1389 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1387 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FUV RELATED DB: PDB REMARK 900 CATALYTIC DOMAIN OF THYMIDINE KINASE FROM TRYPANOSOMA BRUCEI WITH REMARK 900 DTHD REMARK 900 RELATED ID: 5FUX RELATED DB: PDB REMARK 900 CATALYTIC DOMAIN OF THYMIDINE KINASE FROM TRYPANOSOMA BRUCEI WITH REMARK 900 DTMP REMARK 900 RELATED ID: 5FUY RELATED DB: PDB REMARK 900 CATALYTIC DOMAIN OF THYMIDINE KINASE FROM TRYPANOSOMA BRUCEI WITH REMARK 900 DTMP DBREF 5FUW A 203 384 UNP Q38CF2 Q38CF2_TRYB2 203 384 DBREF 5FUW B 203 384 UNP Q38CF2 Q38CF2_TRYB2 203 384 SEQADV 5FUW ASP A 292 UNP Q38CF2 GLY 292 ENGINEERED MUTATION SEQADV 5FUW ASP B 292 UNP Q38CF2 GLY 292 ENGINEERED MUTATION SEQRES 1 A 182 ALA HIS GLY ARG ILE GLU LEU ILE ILE GLY PRO MET PHE SEQRES 2 A 182 ALA GLY LYS THR THR GLU LEU MET ARG ARG VAL GLN ARG SEQRES 3 A 182 HIS LYS HIS ALA GLN ARG SER CYS TYR ILE ILE LYS TYR SEQRES 4 A 182 THR GLY ASP THR ARG TYR SER GLU GLY ALA ILE THR SER SEQRES 5 A 182 HIS ASP GLN ARG ALA LEU THR ALA ASN VAL SER VAL SER SEQRES 6 A 182 ASN LEU HIS ASP VAL GLY ASP GLU TRP ARG LYS TYR ASP SEQRES 7 A 182 VAL ILE ALA VAL ASP GLU GLY GLN PHE PHE PRO ASP VAL SEQRES 8 A 182 ALA ALA PHE CYS SER LYS ALA ALA ASP SER GLY LYS VAL SEQRES 9 A 182 VAL ILE VAL SER ALA LEU ASP ALA ASP TYR LEU GLN GLU SEQRES 10 A 182 PRO PHE GLU GLU ILE CYS LEU LEU VAL SER ARG ALA ASP SEQRES 11 A 182 SER VAL VAL LYS LEU SER ALA VAL CYS MET GLU CYS HIS SEQRES 12 A 182 ASN ARG LYS ALA SER PHE THR TYR ARG THR VAL LYS SER SEQRES 13 A 182 ASP GLU ARG LYS LEU VAL GLY GLY SER ASP MET TYR MET SEQRES 14 A 182 SER VAL CYS ARG SER CYS TYR GLU THR LYS ARG ASN MET SEQRES 1 B 182 ALA HIS GLY ARG ILE GLU LEU ILE ILE GLY PRO MET PHE SEQRES 2 B 182 ALA GLY LYS THR THR GLU LEU MET ARG ARG VAL GLN ARG SEQRES 3 B 182 HIS LYS HIS ALA GLN ARG SER CYS TYR ILE ILE LYS TYR SEQRES 4 B 182 THR GLY ASP THR ARG TYR SER GLU GLY ALA ILE THR SER SEQRES 5 B 182 HIS ASP GLN ARG ALA LEU THR ALA ASN VAL SER VAL SER SEQRES 6 B 182 ASN LEU HIS ASP VAL GLY ASP GLU TRP ARG LYS TYR ASP SEQRES 7 B 182 VAL ILE ALA VAL ASP GLU GLY GLN PHE PHE PRO ASP VAL SEQRES 8 B 182 ALA ALA PHE CYS SER LYS ALA ALA ASP SER GLY LYS VAL SEQRES 9 B 182 VAL ILE VAL SER ALA LEU ASP ALA ASP TYR LEU GLN GLU SEQRES 10 B 182 PRO PHE GLU GLU ILE CYS LEU LEU VAL SER ARG ALA ASP SEQRES 11 B 182 SER VAL VAL LYS LEU SER ALA VAL CYS MET GLU CYS HIS SEQRES 12 B 182 ASN ARG LYS ALA SER PHE THR TYR ARG THR VAL LYS SER SEQRES 13 B 182 ASP GLU ARG LYS LEU VAL GLY GLY SER ASP MET TYR MET SEQRES 14 B 182 SER VAL CYS ARG SER CYS TYR GLU THR LYS ARG ASN MET HET QBT A1386 21 HET PO4 A1387 5 HET PO4 A1388 5 HET ZN A1389 1 HET PO4 B1385 5 HET THM B1386 17 HET ZN B1387 1 HETNAM QBT [(2R,3S,5R)-3-HYDROXY-5-[(5S)-5-METHYL-2,4-DIOXO-1,3- HETNAM 2 QBT DIAZINAN-1-YL]OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE HETNAM PO4 PHOSPHATE ION HETNAM ZN ZINC ION HETNAM THM THYMIDINE HETSYN THM DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE FORMUL 3 QBT C10 H17 N2 O8 P FORMUL 4 PO4 3(O4 P 3-) FORMUL 6 ZN 2(ZN 2+) FORMUL 8 THM C10 H14 N2 O5 FORMUL 10 HOH *147(H2 O) HELIX 1 1 GLY A 217 ALA A 232 1 16 HELIX 2 2 ASN A 268 GLY A 273 5 6 HELIX 3 3 ASP A 274 TYR A 279 5 6 HELIX 4 4 GLY A 287 PHE A 290 5 4 HELIX 5 5 ASP A 292 SER A 303 1 12 HELIX 6 6 PHE A 321 ALA A 331 1 11 HELIX 7 7 CYS A 374 MET A 384 1 11 HELIX 8 8 GLY B 217 ALA B 232 1 16 HELIX 9 9 ASN B 268 GLY B 273 5 6 HELIX 10 10 ASP B 274 TYR B 279 5 6 HELIX 11 11 GLU B 286 PHE B 290 5 5 HELIX 12 12 ASP B 292 SER B 303 1 12 HELIX 13 13 PHE B 321 ALA B 331 1 11 HELIX 14 14 CYS B 374 MET B 384 1 11 SHEET 1 AA 6 ASN A 263 VAL A 266 0 SHEET 2 AA 6 CYS A 236 TYR A 241 1 O ILE A 238 N VAL A 264 SHEET 3 AA 6 VAL A 281 ASP A 285 1 O VAL A 281 N TYR A 237 SHEET 4 AA 6 VAL A 306 SER A 310 1 O VAL A 306 N ILE A 282 SHEET 5 AA 6 ARG A 206 ILE A 211 1 O ARG A 206 N VAL A 307 SHEET 6 AA 6 SER A 333 LYS A 336 1 O SER A 333 N LEU A 209 SHEET 1 AB 2 ALA A 339 VAL A 340 0 SHEET 2 AB 2 LYS A 348 ALA A 349 -1 O ALA A 349 N ALA A 339 SHEET 1 AC 2 PHE A 351 ARG A 354 0 SHEET 2 AC 2 TYR A 370 VAL A 373 -1 O MET A 371 N TYR A 353 SHEET 1 BA 6 ASN B 263 VAL B 266 0 SHEET 2 BA 6 CYS B 236 TYR B 241 1 O ILE B 238 N VAL B 264 SHEET 3 BA 6 VAL B 281 VAL B 284 1 O VAL B 281 N TYR B 237 SHEET 4 BA 6 VAL B 306 SER B 310 1 O VAL B 306 N ILE B 282 SHEET 5 BA 6 ARG B 206 ILE B 211 1 O ARG B 206 N VAL B 307 SHEET 6 BA 6 SER B 333 LYS B 336 1 O SER B 333 N LEU B 209 SHEET 1 BB 2 ALA B 339 VAL B 340 0 SHEET 2 BB 2 LYS B 348 ALA B 349 -1 O ALA B 349 N ALA B 339 SHEET 1 BC 2 PHE B 351 ARG B 354 0 SHEET 2 BC 2 TYR B 370 VAL B 373 -1 O MET B 371 N TYR B 353 SSBOND 1 CYS A 325 CYS B 325 1555 1555 1.96 LINK SG CYS A 341 ZN ZN A1389 1555 1555 2.31 LINK SG CYS A 344 ZN ZN A1389 1555 1555 2.28 LINK SG CYS A 374 ZN ZN A1389 1555 1555 2.26 LINK SG CYS A 377 ZN ZN A1389 1555 1555 2.29 LINK SG CYS B 341 ZN ZN B1387 1555 1555 2.27 LINK SG CYS B 344 ZN ZN B1387 1555 1555 2.28 LINK SG CYS B 374 ZN ZN B1387 1555 1555 2.38 LINK SG CYS B 377 ZN ZN B1387 1555 1555 2.24 SITE 1 AC1 20 LYS A 218 GLU A 286 GLN A 288 PHE A 289 SITE 2 AC1 20 LEU A 312 ASP A 315 TYR A 316 ARG A 354 SITE 3 AC1 20 ARG A 361 LYS A 362 LEU A 363 VAL A 364 SITE 4 AC1 20 GLY A 365 TYR A 370 PO4 A1387 HOH A2006 SITE 5 AC1 20 HOH A2010 HOH A2011 HOH A2031 HOH A2042 SITE 1 AC2 13 PHE A 215 ALA A 216 GLY A 217 LYS A 218 SITE 2 AC2 13 THR A 219 QBT A1386 PO4 A1388 HOH A2006 SITE 3 AC2 13 HOH A2007 HOH A2008 HOH A2009 HOH A2010 SITE 4 AC2 13 HOH A2011 SITE 1 AC3 10 PHE B 215 ALA B 216 GLY B 217 LYS B 218 SITE 2 AC3 10 THR B 219 HOH B2003 HOH B2006 HOH B2008 SITE 3 AC3 10 HOH B2009 HOH B2040 SITE 1 AC4 8 GLY A 217 LYS A 218 THR A 219 THR A 220 SITE 2 AC4 8 PO4 A1387 HOH A2007 HOH A2009 HOH A2011 SITE 1 AC5 15 MET B 214 GLU B 286 GLN B 288 PHE B 289 SITE 2 AC5 15 LEU B 312 ASP B 315 TYR B 316 ARG B 361 SITE 3 AC5 15 LYS B 362 LEU B 363 VAL B 364 GLY B 365 SITE 4 AC5 15 TYR B 370 HOH B2007 HOH B2019 SITE 1 AC6 4 CYS A 341 CYS A 344 CYS A 374 CYS A 377 SITE 1 AC7 4 CYS B 341 CYS B 344 CYS B 374 CYS B 377 CRYST1 114.999 114.999 104.770 90.00 90.00 90.00 P 43 2 2 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 0.008696 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008696 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009545 0.00000