PDB Short entry for 1E2D HEADER PHOSPHOTRANSFERASE 22-MAY-00 1E2D TITLE HUMAN THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE, TITLE 2 ADENOSINE DIPHOSPHATE AND A MAGNESIUM-ION COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMIDYLATE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TMPK; 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; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHOTRANSFERASE, THYMIDYLATE KINASE, P-LOOP EXPDTA X-RAY DIFFRACTION AUTHOR N.OSTERMANN,I.SCHLICHTING,R.BRUNDIERS,M.KONRAD,J.REINSTEIN,T.VEIT, AUTHOR 2 R.S.GOODY,A.LAVIE REVDAT 4 06-MAR-19 1E2D 1 REMARK REVDAT 3 24-FEB-09 1E2D 1 VERSN REVDAT 2 21-FEB-02 1E2D 1 REMARK HET HETNAM HETSYN REVDAT 2 2 1 FORMUL LINK HETATM REVDAT 1 17-MAY-01 1E2D 0 JRNL AUTH N.OSTERMANN,I.SCHLICHTING,R.BRUNDIERS,M.KONRAD,J.REINSTEIN, JRNL AUTH 2 T.VEIT,R.S.GOODY,A.LAVIE JRNL TITL INSIGHTS INTO THE PHOSPHORYLTRANSFER MECHANISM OF HUMAN JRNL TITL 2 THYMIDYLATE KINASE GAINED FROM CRYSTAL STRUCTURES OF ENZYME JRNL TITL 3 COMPLEXES ALONG THE REACTION COORDINATE JRNL REF STRUCTURE V. 8 629 2000 JRNL REFN ISSN 0969-2126 JRNL PMID 10873853 JRNL DOI 10.1016/S0969-2126(00)00149-0 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 27897 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) : 0.201 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 11.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3109 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1646 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 291 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.012 ; NULL REMARK 3 ANGLE DISTANCE (A) : 1.500 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: GLU 152 MODELED AS ALA AND LYS 205 REMARK 3 MODELED AS ALA DUE TO WEAK SIDE-CHAIN ELECTRON DENSITY REMARK 4 REMARK 4 1E2D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAY-00. REMARK 100 THE DEPOSITION ID IS D_1290004861. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-98 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 : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.100 REMARK 200 MONOCHROMATOR : YES REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31064 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 33.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.20300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 3TMK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 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. AN ADP,TMP COCRYSTAL WAS SOAKED OVERNIGHT IN 250 MM NAF REMARK 280 AND 80 MM ALCL3, 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 24.90000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.50000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.35000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.50000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.50000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 12.45000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.50000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.50000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.35000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.50000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.50000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 12.45000 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 24.90000 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 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 101.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 101.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 24.90000 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 REMARK 400 GLY, SER, HIS INSERTED AT THE N-TERMINUS 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 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 GLU A 152 CG CD OE1 OE2 REMARK 470 LYS A 205 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 OE1 GLN A 157 O HOH A 2203 2.15 REMARK 500 OD1 ASP A 15 O HOH A 2031 2.17 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 2243 O HOH A 2285 3554 2.05 REMARK 500 O HOH A 2198 O HOH A 2202 8666 2.11 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 16 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 24 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 41 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 97 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 150 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 150 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 159 CD - NE - CZ ANGL. DEV. = 8.6 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 97 148.18 75.11 REMARK 500 TYR A 98 -145.28 -150.23 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 A2105 DISTANCE = 6.58 ANGSTROMS REMARK 525 HOH A2116 DISTANCE = 6.13 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 ADP A 302 O2B REMARK 620 2 HOH A2280 O 97.3 REMARK 620 3 HOH A2037 O 174.7 88.0 REMARK 620 4 HOH A2274 O 90.8 90.3 89.8 REMARK 620 5 HOH A2290 O 90.2 172.2 84.5 91.4 REMARK 620 6 SER A 20 OG 94.4 86.9 85.3 174.4 90.8 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 A2159 O REMARK 620 2 HOH A2166 O 80.9 REMARK 620 3 HOH A2076 O 89.3 169.9 REMARK 620 4 HOH A2159 O 178.4 99.2 90.5 REMARK 620 5 HOH A2076 O 89.9 87.8 94.9 91.6 REMARK 620 6 HOH A2166 O 96.8 92.1 86.3 81.7 173.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2147 O REMARK 620 2 HOH A2273 O 90.2 REMARK 620 3 HOH A2194 O 88.6 175.4 REMARK 620 4 HOH A2015 O 170.2 81.3 100.3 REMARK 620 5 HOH A2014 O 83.9 86.3 98.0 90.7 REMARK 620 6 HOH A2272 O 83.1 96.5 79.0 102.6 166.7 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 MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TMP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 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: 3TMK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YEAST THYMIDYLATE KINASE COMPLEXED WITH THE REMARK 900 BISUBSTRATE INHIBITOR TP5A AT 2.0 A RESOLUTION: IMPLICATIONS FOR REMARK 900 CATALYSIS AND AZT ACTIVATION REMARK 900 RELATED ID: 2TMK RELATED DB: PDB REMARK 900 YEAST THYMIDYLATE KINASE COMPLEXED WITH 3'-AZIDO-3'-DEOXYTHYMIDINE REMARK 900 MONOPHOSPHATE (AZT-MP) REMARK 900 RELATED ID: 1TMK RELATED DB: PDB REMARK 900 YEAST THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE REMARK 900 (DTMP) 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: 1E2Q RELATED DB: PDB REMARK 900 HUMAN THYMIDYLATE KINASE COMPLEXED WITH TP5A 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: 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 900 RELATED ID: 1E9F RELATED DB: PDB REMARK 900 MUTANT HUMAN THYMIDYLATE KINASE COMPLEXED WITH TMP 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 1E2D A -2 0 PDB 1E2D 1E2D -2 0 DBREF 1E2D A 1 212 UNP P23919 KTHY_HUMAN 1 212 SEQADV 1E2D ALA A 200 UNP P23919 ARG 200 ENGINEERED MUTATION SEQADV 1E2D SER A 183 UNP P23919 ARG 183 CONFLICT SEQADV 1E2D ILE A 184 UNP P23919 LEU 184 CONFLICT SEQADV 1E2D ASP A 190 UNP P23919 GLU 190 CONFLICT SEQADV 1E2D ILE A 191 UNP P23919 LEU 191 CONFLICT SEQRES 1 A 215 GLY SER HIS MET ALA ALA ARG ARG GLY ALA LEU ILE VAL SEQRES 2 A 215 LEU GLU GLY VAL ASP ARG ALA GLY LYS SER THR GLN SER SEQRES 3 A 215 ARG LYS LEU VAL GLU ALA LEU CYS ALA ALA GLY HIS ARG SEQRES 4 A 215 ALA GLU LEU LEU ARG PHE PRO GLU ARG SER THR GLU ILE SEQRES 5 A 215 GLY LYS LEU LEU SER SER TYR LEU GLN LYS LYS SER ASP SEQRES 6 A 215 VAL GLU ASP HIS SER VAL HIS LEU LEU PHE SER ALA ASN SEQRES 7 A 215 ARG TRP GLU GLN VAL PRO LEU ILE LYS GLU LYS LEU SER SEQRES 8 A 215 GLN GLY VAL THR LEU VAL VAL ASP ARG TYR ALA PHE SER SEQRES 9 A 215 GLY VAL ALA PHE THR GLY ALA LYS GLU ASN PHE SER LEU SEQRES 10 A 215 ASP TRP CYS LYS GLN PRO ASP VAL GLY LEU PRO LYS PRO SEQRES 11 A 215 ASP LEU VAL LEU PHE LEU GLN LEU GLN LEU ALA ASP ALA SEQRES 12 A 215 ALA LYS ARG GLY ALA PHE GLY HIS GLU ARG TYR GLU ASN SEQRES 13 A 215 GLY ALA PHE GLN GLU ARG ALA LEU ARG CYS PHE HIS GLN SEQRES 14 A 215 LEU MET LYS ASP THR THR LEU ASN TRP LYS MET VAL ASP SEQRES 15 A 215 ALA SER LYS SER ILE GLU ALA VAL HIS GLU ASP ILE ARG SEQRES 16 A 215 VAL LEU SER GLU ASP ALA ILE ALA THR ALA THR GLU LYS SEQRES 17 A 215 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 HET MG A 403 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 3(MG 2+) FORMUL 7 HOH *291(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 ALA A 108 1 11 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 LYS A 142 1 7 HELIX 9 9 ASN A 153 MET A 168 1 16 HELIX 10 10 SER A 183 THR A 203 1 21 SHEET 1 A 5 TRP A 175 ASP A 179 0 SHEET 2 A 5 LEU A 129 GLN A 134 1 N VAL A 130 O LYS A 176 SHEET 3 A 5 LEU A 8 GLY A 13 1 N VAL A 10 O LEU A 129 SHEET 4 A 5 THR A 92 ASP A 96 1 N LEU A 93 O ILE A 9 SHEET 5 A 5 ALA A 37 ARG A 41 1 N GLU A 38 O THR A 92 LINK O2B ADP A 302 MG MG A 401 1555 1555 2.03 LINK MG MG A 401 O HOH A2280 1555 1555 2.12 LINK MG MG A 401 O HOH A2037 1555 1555 2.11 LINK MG MG A 401 O HOH A2274 1555 1555 2.12 LINK MG MG A 401 O HOH A2290 1555 1555 2.06 LINK MG MG A 401 OG SER A 20 1555 1555 2.13 LINK MG MG A 402 O HOH A2159 1555 1555 2.09 LINK MG MG A 402 O HOH A2166 1555 8665 1.94 LINK MG MG A 402 O HOH A2076 1555 1555 2.06 LINK MG MG A 402 O HOH A2159 1555 8665 2.04 LINK MG MG A 402 O HOH A2076 1555 8665 2.03 LINK MG MG A 402 O HOH A2166 1555 1555 1.96 LINK MG MG A 403 O HOH A2147 1555 1555 2.36 LINK MG MG A 403 O HOH A2273 1555 1555 2.18 LINK MG MG A 403 O HOH A2194 1555 1555 2.12 LINK MG MG A 403 O HOH A2015 1555 1555 2.26 LINK MG MG A 403 O HOH A2014 1555 1555 2.18 LINK MG MG A 403 O HOH A2272 1555 1555 2.29 CISPEP 1 PHE A 42 PRO A 43 0 0.63 SITE 1 AC1 6 SER A 20 ADP A 302 HOH A2037 HOH A2274 SITE 2 AC1 6 HOH A2280 HOH A2290 SITE 1 AC2 3 HOH A2076 HOH A2159 HOH A2166 SITE 1 AC3 6 HOH A2014 HOH A2015 HOH A2147 HOH A2194 SITE 2 AC3 6 HOH A2272 HOH A2273 SITE 1 AC4 20 PHE A 42 ARG A 45 LEU A 57 PHE A 72 SITE 2 AC4 20 ARG A 76 ARG A 97 GLY A 102 PHE A 105 SITE 3 AC4 20 TYR A 151 HOH A2037 HOH A2204 HOH A2272 SITE 4 AC4 20 HOH A2273 HOH A2274 HOH A2275 HOH A2276 SITE 5 AC4 20 HOH A2277 HOH A2278 HOH A2279 HOH A2280 SITE 1 AC5 26 ARG A 16 ALA A 17 GLY A 18 LYS A 19 SITE 2 AC5 26 SER A 20 THR A 21 ARG A 143 ALA A 180 SITE 3 AC5 26 LYS A 182 SER A 183 ILE A 184 ARG A 192 SITE 4 AC5 26 MG A 401 HOH A2030 HOH A2044 HOH A2274 SITE 5 AC5 26 HOH A2282 HOH A2283 HOH A2284 HOH A2285 SITE 6 AC5 26 HOH A2286 HOH A2287 HOH A2288 HOH A2289 SITE 7 AC5 26 HOH A2290 HOH A2291 CRYST1 101.000 101.000 49.800 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 0.009901 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009901 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020080 0.00000