HEADER TRANSFERASE 18-SEP-02 1MRN TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE TITLE 2 COMPLEXED WITH BISUBSTRATE INHIBITOR (TP5A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMIDYLATE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DTMP KINASE, THYMIDYLIC KINASE, TMPK; COMPND 5 EC: 2.7.4.9; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS TRANSFERASE (ATP:TMP PHOSPHOTRANSFERASE), KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.HAOUZ,V.VANHEUSDEN,H.MUNIER-LEHMANN,M.FROEYEN,P.HERDEWIJN,S.VAN AUTHOR 2 CALENBERGH,M.DELARUE REVDAT 4 14-FEB-24 1MRN 1 REMARK LINK REVDAT 3 24-FEB-09 1MRN 1 VERSN REVDAT 2 14-DEC-04 1MRN 1 JRNL REVDAT 1 07-JAN-03 1MRN 0 JRNL AUTH A.HAOUZ,V.VANHEUSDEN,H.MUNIER-LEHMANN,M.FROEYEN,P.HERDEWIJN, JRNL AUTH 2 S.VAN CALENBERGH,M.DELARUE JRNL TITL ENZYMATIC AND STRUCTURAL ANALYSIS OF INHIBITORS DESIGNED JRNL TITL 2 AGAINST MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE. NEW JRNL TITL 3 INSIGHTS INTO THE PHOSPHORYL TRANSFER MECHANISM. JRNL REF J.BIOL.CHEM. V. 278 4963 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12454011 JRNL DOI 10.1074/JBC.M209630200 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.100 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 8139 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 SET) : 0.236 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 379 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.54 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 688 REMARK 3 BIN R VALUE (WORKING SET) : 0.3076 REMARK 3 BIN FREE R VALUE : 0.2864 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 23 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1542 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 58 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.08 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM SIGMAA (A) : 0.32 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.44 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.36 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.206 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.08 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.761 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 42.56 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MRN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-SEP-02. REMARK 100 THE DEPOSITION ID IS D_1000017131. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JAN-02 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8407 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 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 (%) : 92.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : 0.06600 REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.36600 REMARK 200 R SYM FOR SHELL (I) : 0.36600 REMARK 200 FOR SHELL : 9.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1G3U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PEG600, MES, REMARK 280 MAGNESIUM ACETATE, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 88.89333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.44667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 66.67000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.22333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 111.11667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 88.89333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 44.44667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 22.22333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 66.67000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 111.11667 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 300 REMARK: THE MOLECULE IS NORMALLY A DIMER IN SOLUTION. THE OTHER REMARK 300 MONOMER (B) CAN BE GENERATED BY APPLYING THE TRANSFORMATION X, -Y, - REMARK 300 Z TO MOLECULE A. 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 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 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 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 PRO A 209 REMARK 465 PRO A 210 REMARK 465 ASP A 211 REMARK 465 VAL A 212 REMARK 465 PRO A 213 REMARK 465 SER A 214 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 ARG A 86 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 144 CG CD OE1 OE2 REMARK 470 LEU A 145 CG CD1 CD2 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 NH1 ARG A 14 NH1 ARG A 14 10665 1.72 REMARK 500 O HOH A 314 O HOH A 314 10665 2.00 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 VAL A 8 174.53 -58.35 REMARK 500 ALA A 27 25.25 -140.61 REMARK 500 HIS A 56 61.33 61.12 REMARK 500 ARG A 95 138.42 82.13 REMARK 500 TYR A 96 -147.76 -146.23 REMARK 500 LEU A 139 87.03 -69.05 REMARK 500 ALA A 161 144.18 171.60 REMARK 500 VAL A 194 -142.48 -98.71 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 MG A 300 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 9 OD1 REMARK 620 2 GLU A 166 OE2 107.8 REMARK 620 3 T5A A 301 O1B 166.2 71.9 REMARK 620 4 T5A A 301 O2A 70.8 167.7 106.4 REMARK 620 5 T5A A 301 O3A 115.9 131.9 60.8 45.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 220 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE T5A A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G3U RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE REMARK 900 COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP) REMARK 900 RELATED ID: 1MRS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE REMARK 900 COMPLEXED WITH 5-CH2OH DEOXYURIDINE MONOPHOSPHATE DBREF 1MRN A 1 214 UNP O05891 KTHY_MYCTU 1 214 SEQRES 1 A 214 MET LEU ILE ALA ILE GLU GLY VAL ASP GLY ALA GLY LYS SEQRES 2 A 214 ARG THR LEU VAL GLU LYS LEU SER GLY ALA PHE ARG ALA SEQRES 3 A 214 ALA GLY ARG SER VAL ALA THR LEU ALA PHE PRO ARG TYR SEQRES 4 A 214 GLY GLN SER VAL ALA ALA ASP ILE ALA ALA GLU ALA LEU SEQRES 5 A 214 HIS GLY GLU HIS GLY ASP LEU ALA SER SER VAL TYR ALA SEQRES 6 A 214 MET ALA THR LEU PHE ALA LEU ASP ARG ALA GLY ALA VAL SEQRES 7 A 214 HIS THR ILE GLN GLY LEU CYS ARG GLY TYR ASP VAL VAL SEQRES 8 A 214 ILE LEU ASP ARG TYR VAL ALA SER ASN ALA ALA TYR SER SEQRES 9 A 214 ALA ALA ARG LEU HIS GLU ASN ALA ALA GLY LYS ALA ALA SEQRES 10 A 214 ALA TRP VAL GLN ARG ILE GLU PHE ALA ARG LEU GLY LEU SEQRES 11 A 214 PRO LYS PRO ASP TRP GLN VAL LEU LEU ALA VAL SER ALA SEQRES 12 A 214 GLU LEU ALA GLY GLU ARG SER ARG GLY ARG ALA GLN ARG SEQRES 13 A 214 ASP PRO GLY ARG ALA ARG ASP ASN TYR GLU ARG ASP ALA SEQRES 14 A 214 GLU LEU GLN GLN ARG THR GLY ALA VAL TYR ALA GLU LEU SEQRES 15 A 214 ALA ALA GLN GLY TRP GLY GLY ARG TRP LEU VAL VAL GLY SEQRES 16 A 214 ALA ASP VAL ASP PRO GLY ARG LEU ALA ALA THR LEU ALA SEQRES 17 A 214 PRO PRO ASP VAL PRO SER HET SO4 A 219 5 HET SO4 A 220 5 HET MG A 300 1 HET T5A A 301 55 HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION HETNAM T5A P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 MG MG 2+ FORMUL 5 T5A C20 H30 N7 O23 P5 FORMUL 6 HOH *58(H2 O) HELIX 1 1 GLY A 12 ALA A 26 1 15 HELIX 2 2 SER A 42 HIS A 53 1 12 HELIX 3 3 ASP A 58 SER A 61 5 4 HELIX 4 4 SER A 62 GLY A 76 1 15 HELIX 5 5 ALA A 77 TYR A 88 1 12 HELIX 6 6 TYR A 96 LEU A 108 1 13 HELIX 7 7 GLY A 114 PHE A 125 1 12 HELIX 8 8 SER A 142 ASP A 157 1 16 HELIX 9 9 ASP A 163 ASP A 168 1 6 HELIX 10 10 ASP A 168 GLN A 185 1 18 HELIX 11 11 ASP A 199 LEU A 207 1 9 SHEET 1 A 5 VAL A 31 ALA A 35 0 SHEET 2 A 5 VAL A 90 ASP A 94 1 O ILE A 92 N ALA A 32 SHEET 3 A 5 LEU A 2 GLU A 6 1 N ILE A 5 O LEU A 93 SHEET 4 A 5 TRP A 135 LEU A 138 1 O VAL A 137 N GLU A 6 SHEET 5 A 5 ARG A 190 VAL A 193 1 O LEU A 192 N GLN A 136 LINK OD1 ASP A 9 MG MG A 300 1555 1555 1.97 LINK OE2 GLU A 166 MG MG A 300 1555 1555 2.32 LINK MG MG A 300 O1B T5A A 301 1555 1555 2.65 LINK MG MG A 300 O2A T5A A 301 1555 1555 2.93 LINK MG MG A 300 O3A T5A A 301 1555 1555 2.36 CISPEP 1 PHE A 36 PRO A 37 0 1.13 SITE 1 AC1 10 GLN A 121 LYS A 132 ALA A 154 GLN A 155 SITE 2 AC1 10 ALA A 161 ARG A 162 ARG A 167 TRP A 187 SITE 3 AC1 10 GLY A 188 HOH A 311 SITE 1 AC2 7 GLY A 10 ALA A 11 GLY A 12 LYS A 13 SITE 2 AC2 7 ARG A 14 ARG A 153 HOH A 306 SITE 1 AC3 3 ASP A 9 GLU A 166 T5A A 301 SITE 1 AC4 27 ASP A 9 PRO A 37 TYR A 39 ALA A 49 SITE 2 AC4 27 GLU A 50 HIS A 53 GLU A 55 PHE A 70 SITE 3 AC4 27 ARG A 74 ARG A 95 SER A 99 ASN A 100 SITE 4 AC4 27 TYR A 103 ARG A 122 ARG A 160 ASP A 163 SITE 5 AC4 27 TYR A 165 GLU A 166 MG A 300 HOH A 306 SITE 6 AC4 27 HOH A 309 HOH A 318 HOH A 328 HOH A 329 SITE 7 AC4 27 HOH A 331 HOH A 334 HOH A 359 CRYST1 75.460 75.460 133.340 90.00 90.00 120.00 P 65 2 2 12 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 0.013252 0.007651 0.000000 0.00000 SCALE2 0.000000 0.015302 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007500 0.00000