HEADER TRANSFERASE 11-OCT-00 1E9F TITLE MUTANT HUMAN THYMIDYLATE KINASE COMPLEXED WITH TMP AND ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMIDYLATE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DTMP KINASE; COMPND 5 EC: 2.7.4.9; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS, ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 9606, 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHOTRANSFERASE, THYMIDYLATE KINASE, P-LOOP, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR N.OSTERMANN,A.LAVIE,S.PADIYAR,R.BRUNDIERS,T.VEIT,J.REINSTEIN, AUTHOR 2 R.S.GOODY,M.KONRAD,I.SCHLICHTING REVDAT 7 08-MAY-24 1E9F 1 REMARK LINK REVDAT 6 24-JUL-19 1E9F 1 REMARK REVDAT 5 06-MAR-19 1E9F 1 REMARK REVDAT 4 15-MAR-17 1E9F 1 SOURCE REVDAT 3 24-FEB-09 1E9F 1 VERSN REVDAT 2 18-JUL-03 1E9F 1 REMARK REVDAT 1 11-OCT-01 1E9F 0 JRNL AUTH N.OSTERMANN,A.LAVIE,S.PADIYAR,R.BRUNDIERS,T.VEIT,J.REINTEIN, JRNL AUTH 2 R.S.GOODY,M.KONRAD,I.SCHLICHTING JRNL TITL POTENTIATING AZT ACTIVATION: STRUCTURES OF WILDTYPE AND JRNL TITL 2 MUTANT HUMAN THYMIDYLATE KINASE SUGGEST REASONS FOR THE JRNL TITL 3 MUTANTS' IMPROVED KINETICS WITH THE HIV PRODRUG METABOLITE JRNL TITL 4 AZTMP JRNL REF J.MOL.BIOL. V. 304 43 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 11071809 JRNL DOI 10.1006/JMBI.2000.4175 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.OSTERMANN,I.SCHLICHTING,R.BRUNDIERS,M.KONRAD,J.REINSTEIN, REMARK 1 AUTH 2 T.VEIT,R.S.GOODY,A.LAVIE REMARK 1 TITL INSIGHTS INTO THE PHOSPHORYLTRANSFER MECHANISM OF HUMAN REMARK 1 TITL 2 THYMIDYLATE KINASE GAINED FROM CRYSTAL STRUCTURES OF ENZYME REMARK 1 TITL 3 COMPLEXES ALONG THE REACTION COORDINATE. REMARK 1 REF STRUCTURE V. 8 629 2000 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 10873853 REMARK 1 DOI 10.1016/S0969-2126(00)00149-0 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 19650 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2019 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1577 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 162 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1E9F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1290005442. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8443 REMARK 200 MONOCHROMATOR : YES REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19646 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 70.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05400 REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.14400 REMARK 200 FOR SHELL : 3.200 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION AT 293 K MIXING 2 REMARK 280 MICROLITERS OF A SOLUTION CONTAINING THE ENZYME, NUCLEOTIDES, REMARK 280 AND 50 MM MGCL2 WITH 2 MICROLITERS OF A SOLUTION CONTAINING 21% REMARK 280 PEG 3350, 100 MM TRIS HCL PH 8.0 AND 50 MICROLITERS OF DEAD SEA REMARK 280 WATER., PH 8.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.60000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.10000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.10000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.90000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.10000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.10000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 12.30000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.10000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.10000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 36.90000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.10000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.10000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 12.30000 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 0.00000 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 24.60000 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.9 KCAL/MOL 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 BIOMT1 2 0.000000 -1.000000 0.000000 100.20000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 100.20000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 24.60000 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 MG MG A 402 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 CHAIN A - ENGINEERED MUTATION ARG200ALA, ARG16GLY REMARK 400 CHAIN A - (GLY SER HIS) INSERTED AT THE N-TERMINUS REMARK 400 CONVERSION OF DTMP TO DTDP REMARK 400 ATP + THYMIDINE 5'-MONOPHOSPHATE = ADP + THYMIDINE 5'-DIPHOSPHATE. REMARK 400 REMARK 400 IN THIS MUTANT THE SO-CALLED LID REGION (RESIDUES REMARK 400 A145-A148) HAS BEEN SUBSTITUTED WITH THE CORRESPONDING, REMARK 400 SLIGHTLY LONGER SEQUENCE (RESIDUES 151-156 RARGEL) FROM THE REMARK 400 E.COLI ENZYME. THESE RESIDUES ARE NOT VISIBLE IN THE REMARK 400 ELECTRON DENSITY. THEREFORE, THE RESIDUES HAVE NOT BEEN REMARK 400 RENUMBERED. 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 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 ALA A 3 REMARK 465 GLY A 144 REMARK 465 ARG A 145 REMARK 465 ALA A 146 REMARK 465 ARG A 147 REMARK 465 GLY A 148 REMARK 465 GLU A 148A REMARK 465 LEU A 148B REMARK 465 GLU A 149 REMARK 465 ARG A 150 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 142 CG CD CE NZ REMARK 470 TYR A 151 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 152 CG CD OE1 OE2 REMARK 470 LYS A 212 O 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 CB TYR A 151 O HOH A 2108 0.21 REMARK 500 OE2 GLU A 48 O HOH A 2045 0.88 REMARK 500 CD GLU A 48 O HOH A 2045 1.17 REMARK 500 OG SER A 61 O HOH A 2052 1.26 REMARK 500 OE1 GLU A 185 O HOH A 2128 1.37 REMARK 500 CA TYR A 151 O HOH A 2108 1.37 REMARK 500 NH1 ARG A 41 O HOH A 2035 1.38 REMARK 500 NZ LYS A 126 O HOH A 2098 1.44 REMARK 500 CG GLU A 48 O HOH A 2045 1.79 REMARK 500 OE2 GLU A 189 O HOH A 2131 2.13 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 24 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 41 CD - NE - CZ ANGL. DEV. = 18.4 DEGREES REMARK 500 ARG A 41 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 76 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 97 CD - NE - CZ ANGL. DEV. = 24.3 DEGREES REMARK 500 ARG A 97 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 TYR A 98 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 TYR A 98 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 143 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 159 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 ALA A 200 CB - CA - C ANGL. DEV. = -9.8 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 97 140.41 82.81 REMARK 500 TYR A 98 -143.87 -145.18 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 A2020 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A2066 DISTANCE = 5.92 ANGSTROMS 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 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 20 OG REMARK 620 2 ADP A 302 O2B 92.2 REMARK 620 3 HOH A2014 O 85.7 175.6 REMARK 620 4 HOH A2082 O 82.2 94.1 81.8 REMARK 620 5 HOH A2155 O 175.2 91.0 90.8 94.0 REMARK 620 6 HOH A2156 O 81.8 96.2 87.4 161.3 101.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2040 O REMARK 620 2 HOH A2040 O 79.3 REMARK 620 3 HOH A2089 O 167.5 90.7 REMARK 620 4 HOH A2089 O 91.5 167.1 99.5 REMARK 620 5 HOH A2093 O 77.8 106.9 98.2 79.6 REMARK 620 6 HOH A2093 O 106.2 76.8 78.5 97.5 175.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TMP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1E2D RELATED DB: PDB REMARK 900 HUMAN THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE, REMARK 900 ADENOSINE DIPHOSPHATE AND A MAGNESIUM-ION REMARK 900 RELATED ID: 1E2E RELATED DB: PDB REMARK 900 HUMAN THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE, REMARK 900 ADENOSINE DIPHOSPHATE,A MAGNESIUM-ION AND ALF3 REMARK 900 RELATED ID: 1E2F RELATED DB: PDB REMARK 900 HUMAN THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE, REMARK 900 ADENOSINE DIPHOSPHATE AND A MAGNESIUM-ION REMARK 900 RELATED ID: 1E2G RELATED DB: PDB REMARK 900 HUMAN THYMIDYLATE KINASE COMPLEXED WITH ADP, TDP AND A MAGNESIUM-ION REMARK 900 RELATED ID: 1E2Q RELATED DB: PDB REMARK 900 HUMAN THYMIDYLATE KINASE COMPLEXED WITH TP5A AND A MAGNESIUM-ION REMARK 900 RELATED ID: 1E98 RELATED DB: PDB REMARK 900 WILD TYPE HUMAN THYMIDYLATE KINASE COMPLEXED WITH AZTMP AND ADP REMARK 900 RELATED ID: 1E99 RELATED DB: PDB REMARK 900 HUMAN THYMIDYLATE KINASE COMPLEXED WITH AZTMP AND ADP REMARK 900 RELATED ID: 1E9A RELATED DB: PDB REMARK 900 HUMAN THYMIDYLATE KINASE COMPLEXED WITH THE BISUBSTRATE INHIBITOR REMARK 900 AZTP5A REMARK 900 RELATED ID: 1E9B RELATED DB: PDB REMARK 900 HUMAN THYMIDYLATE KINASE COMPLEXED WITH AZTMP AND APPNP REMARK 900 RELATED ID: 1E9C RELATED DB: PDB REMARK 900 MUTANT HUMAN THYMIDYLATE KINASE COMPLEXED WITH TMP AND APPNP REMARK 900 RELATED ID: 1E9D RELATED DB: PDB REMARK 900 MUTANT HUMAN THYMIDYLATE KINASE (F105Y) COMPLEXED WITH AZTMP AND ADP REMARK 900 RELATED ID: 1E9E RELATED DB: PDB REMARK 900 MUTANT HUMAN THYMIDYLATE KINASE (F105Y) COMPLEXED WITH DTMP AND ADP REMARK 999 REMARK 999 SEQUENCE REMARK 999 SAMPLE COMTAINS SER183, ILE184, ASP190, AND A ILE191 REMARK 999 (CONFIRMED BY THE DNA SEQUENCE AND ELECTRON DENSITY OF REMARK 999 SIDE-CHAINS). POSSIBLE ERROR IN SWISSPROT ENTRY. DBREF 1E9F A 1 144 UNP P23919 KTHY_HUMAN 1 144 DBREF 1E9F A 145 148B UNP P37345 KTHY_ECOLI 151 156 DBREF 1E9F A 149 212 UNP P23919 KTHY_HUMAN 149 212 SEQADV 1E9F GLY A -2 UNP P23919 EXPRESSION TAG SEQADV 1E9F SER A -1 UNP P23919 EXPRESSION TAG SEQADV 1E9F HIS A 0 UNP P23919 EXPRESSION TAG SEQADV 1E9F ALA A 200 UNP P23919 ARG 200 ENGINEERED MUTATION SEQADV 1E9F GLY A 16 UNP P23919 ARG 16 ENGINEERED MUTATION SEQADV 1E9F ILE A 184 UNP P23919 LEU 184 CONFLICT SEQADV 1E9F ILE A 191 UNP P23919 LEU 191 CONFLICT SEQADV 1E9F ASP A 190 UNP P23919 GLU 190 CONFLICT SEQADV 1E9F SER A 183 UNP P23919 ARG 183 CONFLICT SEQRES 1 A 217 GLY SER HIS MET ALA ALA ARG ARG GLY ALA LEU ILE VAL SEQRES 2 A 217 LEU GLU GLY VAL ASP GLY ALA GLY LYS SER THR GLN SER SEQRES 3 A 217 ARG LYS LEU VAL GLU ALA LEU CYS ALA ALA GLY HIS ARG SEQRES 4 A 217 ALA GLU LEU LEU ARG PHE PRO GLU ARG SER THR GLU ILE SEQRES 5 A 217 GLY LYS LEU LEU SER SER TYR LEU GLN LYS LYS SER ASP SEQRES 6 A 217 VAL GLU ASP HIS SER VAL HIS LEU LEU PHE SER ALA ASN SEQRES 7 A 217 ARG TRP GLU GLN VAL PRO LEU ILE LYS GLU LYS LEU SER SEQRES 8 A 217 GLN GLY VAL THR LEU VAL VAL ASP ARG TYR ALA PHE SER SEQRES 9 A 217 GLY VAL ALA PHE THR GLY ALA LYS GLU ASN PHE SER LEU SEQRES 10 A 217 ASP TRP CYS LYS GLN PRO ASP VAL GLY LEU PRO LYS PRO SEQRES 11 A 217 ASP LEU VAL LEU PHE LEU GLN LEU GLN LEU ALA ASP ALA SEQRES 12 A 217 ALA LYS ARG GLY ARG ALA ARG GLY GLU LEU GLU ARG TYR SEQRES 13 A 217 GLU ASN GLY ALA PHE GLN GLU ARG ALA LEU ARG CYS PHE SEQRES 14 A 217 HIS GLN LEU MET LYS ASP THR THR LEU ASN TRP LYS MET SEQRES 15 A 217 VAL ASP ALA SER LYS SER ILE GLU ALA VAL HIS GLU ASP SEQRES 16 A 217 ILE ARG VAL LEU SER GLU ASP ALA ILE ALA THR ALA THR SEQRES 17 A 217 GLU LYS PRO LEU GLY GLU LEU TRP LYS HET TMP A 301 21 HET ADP A 302 27 HET MG A 401 1 HET MG A 402 1 HETNAM TMP THYMIDINE-5'-PHOSPHATE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 TMP C10 H15 N2 O8 P FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 MG 2(MG 2+) FORMUL 6 HOH *162(H2 O) HELIX 1 1 GLY A 18 ALA A 33 1 16 HELIX 2 2 THR A 47 GLN A 58 1 12 HELIX 3 3 GLU A 64 GLU A 78 1 15 HELIX 4 4 GLN A 79 GLN A 89 1 11 HELIX 5 5 TYR A 98 GLY A 107 1 10 HELIX 6 6 SER A 113 GLN A 119 1 7 HELIX 7 7 PRO A 120 VAL A 122 5 3 HELIX 8 8 GLN A 136 ARG A 143 1 8 HELIX 9 9 ASN A 153 MET A 168 1 16 HELIX 10 10 SER A 183 THR A 201 1 19 HELIX 11 11 ALA A 202 LYS A 205 5 4 SHEET 1 A 5 ALA A 37 ARG A 41 0 SHEET 2 A 5 THR A 92 ASP A 96 1 O THR A 92 N GLU A 38 SHEET 3 A 5 LEU A 8 GLU A 12 1 O ILE A 9 N VAL A 95 SHEET 4 A 5 LEU A 129 GLN A 134 1 O LEU A 129 N VAL A 10 SHEET 5 A 5 TRP A 175 ASP A 179 1 O LYS A 176 N PHE A 132 LINK OG SER A 20 MG MG A 401 1555 1555 2.12 LINK O2B ADP A 302 MG MG A 401 1555 1555 2.02 LINK MG MG A 401 O HOH A2014 1555 1555 2.43 LINK MG MG A 401 O HOH A2082 1555 1555 2.36 LINK MG MG A 401 O HOH A2155 1555 1555 2.32 LINK MG MG A 401 O HOH A2156 1555 1555 2.36 LINK MG MG A 402 O HOH A2040 1555 8665 2.36 LINK MG MG A 402 O HOH A2040 1555 1555 2.37 LINK MG MG A 402 O HOH A2089 1555 8665 2.25 LINK MG MG A 402 O HOH A2089 1555 1555 2.24 LINK MG MG A 402 O HOH A2093 1555 8665 2.56 LINK MG MG A 402 O HOH A2093 1555 1555 2.60 CISPEP 1 PHE A 42 PRO A 43 0 -0.91 SITE 1 AC1 6 SER A 20 ADP A 302 HOH A2014 HOH A2082 SITE 2 AC1 6 HOH A2155 HOH A2156 SITE 1 AC2 3 HOH A2040 HOH A2089 HOH A2093 SITE 1 AC3 13 ASP A 15 PHE A 42 LEU A 57 PHE A 72 SITE 2 AC3 13 ARG A 76 ARG A 97 GLY A 102 PHE A 105 SITE 3 AC3 13 HOH A2037 HOH A2082 HOH A2153 HOH A2154 SITE 4 AC3 13 HOH A2155 SITE 1 AC4 20 GLY A 16 ALA A 17 GLY A 18 LYS A 19 SITE 2 AC4 20 SER A 20 THR A 21 ARG A 143 LYS A 182 SITE 3 AC4 20 SER A 183 ILE A 184 ARG A 192 MG A 401 SITE 4 AC4 20 HOH A2107 HOH A2155 HOH A2156 HOH A2157 SITE 5 AC4 20 HOH A2158 HOH A2160 HOH A2161 HOH A2162 CRYST1 100.200 100.200 49.200 90.00 90.00 90.00 P 43 21 2 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 0.009980 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009980 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020325 0.00000