HEADER TRANSFERASE 08-NOV-10 2XX3 TITLE HUMAN THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE BUTENYL TITLE 2 PHOSPHONATE MONOPHOSPHATE 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 OTHER_DETAILS: 6 HISTIDINE TAG 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 TRANSFERASE, ACYCLIC NUCLEOSIDE PHOSPHONATE EXPDTA X-RAY DIFFRACTION AUTHOR C.CAILLAT,P.MEYER REVDAT 1 07-DEC-11 2XX3 0 JRNL AUTH D.TOPALIS,U.PRADERE,V.ROY,C.CAILLAT,A.AZZOUZI,J.BROGGI, JRNL AUTH 2 R.SNOECK,G.ANDREI,J.LIN,S.ERIKSSON,J.A.C.ALEXANDRE, JRNL AUTH 3 C.EL-AMRI,D.DEVILLE-BONNE,P.MEYER,J.BALZARINI,L.A.AGROFOGLIO JRNL TITL NOVEL ANTIVIRAL C5-SUBSTITUTED PYRIMIDINE ACYCLIC JRNL TITL 2 NUCLEOSIDE PHOSPHONATES SELECTED AS HUMAN THYMIDYLATE JRNL TITL 3 KINASE SUBSTRATES. JRNL REF J.MED.CHEM. V. 54 222 2011 JRNL REFN ISSN 0022-2623 JRNL PMID 21128666 JRNL DOI 10.1021/JM1011462 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.8.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SMART,VONRHEIN,WOMACK, REMARK 3 : MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 15820 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) : 0.1911 REMARK 3 R VALUE (WORKING SET) : 0.1881 REMARK 3 FREE R VALUE : 0.2354 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.33 REMARK 3 FREE R VALUE TEST SET COUNT : 1001 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.14 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2809 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2174 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2646 REMARK 3 BIN R VALUE (WORKING SET) : 0.2166 REMARK 3 BIN FREE R VALUE : 0.2301 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 163 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 : 1586 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 203 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.74 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.4355 REMARK 3 B22 (A**2) : -0.4645 REMARK 3 B33 (A**2) : 0.9000 REMARK 3 B12 (A**2) : 0.0000 REMARK 3 B13 (A**2) : 1.9004 REMARK 3 B23 (A**2) : 0.0000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.245 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.194 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.169 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.178 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.163 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.9307 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.8841 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1667 ; 2.00 ; HARMONIC REMARK 3 BOND ANGLES : 2254 ; 2.00 ; HARMONIC REMARK 3 TORSION ANGLES : 592 ; 2.00 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 45 ; 2.00 ; HARMONIC REMARK 3 GENERAL PLANES : 238 ; 5.00 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1646 ; 20.00 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.00 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : 4 ; 0.00 ; HARMONIC REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 202 ; 5.00 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2094 ; 4.00 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.00 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.24 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.76 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 3-40) REMARK 3 ORIGIN FOR THE GROUP (A): -13.5576 10.2550 5.7779 REMARK 3 T TENSOR REMARK 3 T11: -0.1080 T22: 0.1429 REMARK 3 T33: -0.1231 T12: -0.0075 REMARK 3 T13: -0.0017 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 1.6548 L22: 0.7616 REMARK 3 L33: 2.9962 L12: -0.9299 REMARK 3 L13: 0.4168 L23: 0.7945 REMARK 3 S TENSOR REMARK 3 S11: 0.0474 S12: 0.0297 S13: -0.0695 REMARK 3 S21: 0.0051 S22: -0.0140 S23: 0.0691 REMARK 3 S31: 0.0959 S32: 0.2003 S33: -0.0334 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 41-53) REMARK 3 ORIGIN FOR THE GROUP (A): -18.8253 2.1017 21.2244 REMARK 3 T TENSOR REMARK 3 T11: -0.0500 T22: 0.1347 REMARK 3 T33: -0.0607 T12: 0.0376 REMARK 3 T13: -0.0323 T23: 0.0251 REMARK 3 L TENSOR REMARK 3 L11: 0.8423 L22: 1.0966 REMARK 3 L33: -0.1557 L12: 0.1381 REMARK 3 L13: 0.1547 L23: -0.3547 REMARK 3 S TENSOR REMARK 3 S11: -0.0195 S12: 0.0035 S13: -0.0190 REMARK 3 S21: 0.0555 S22: 0.0171 S23: 0.0497 REMARK 3 S31: 0.0534 S32: 0.0230 S33: 0.0025 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 54-72) REMARK 3 ORIGIN FOR THE GROUP (A): -26.6281 9.5963 28.1026 REMARK 3 T TENSOR REMARK 3 T11: -0.1063 T22: 0.2271 REMARK 3 T33: -0.1405 T12: 0.0050 REMARK 3 T13: -0.0570 T23: -0.0292 REMARK 3 L TENSOR REMARK 3 L11: 0.7721 L22: 0.0000 REMARK 3 L33: 0.9607 L12: 0.0681 REMARK 3 L13: 0.4744 L23: 0.1716 REMARK 3 S TENSOR REMARK 3 S11: -0.0229 S12: -0.0118 S13: -0.0153 REMARK 3 S21: 0.0110 S22: -0.0169 S23: 0.0528 REMARK 3 S31: 0.0200 S32: 0.0168 S33: 0.0398 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 73-131) REMARK 3 ORIGIN FOR THE GROUP (A): -16.5727 14.8675 19.1833 REMARK 3 T TENSOR REMARK 3 T11: -0.1025 T22: 0.1839 REMARK 3 T33: -0.1627 T12: -0.0160 REMARK 3 T13: -0.0097 T23: -0.0047 REMARK 3 L TENSOR REMARK 3 L11: 1.7520 L22: 1.0424 REMARK 3 L33: 3.0003 L12: -0.3683 REMARK 3 L13: -0.5136 L23: 0.4013 REMARK 3 S TENSOR REMARK 3 S11: 0.0753 S12: -0.0873 S13: -0.1596 REMARK 3 S21: 0.0667 S22: -0.0751 S23: -0.0320 REMARK 3 S31: 0.0054 S32: 0.0804 S33: -0.0002 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 132-157) REMARK 3 ORIGIN FOR THE GROUP (A): -33.9555 11.8259 7.6630 REMARK 3 T TENSOR REMARK 3 T11: -0.1147 T22: 0.2443 REMARK 3 T33: -0.1284 T12: 0.0065 REMARK 3 T13: -0.0102 T23: -0.0467 REMARK 3 L TENSOR REMARK 3 L11: 1.9423 L22: 0.0099 REMARK 3 L33: 0.9903 L12: -0.7444 REMARK 3 L13: -0.0975 L23: -1.1841 REMARK 3 S TENSOR REMARK 3 S11: 0.0186 S12: 0.0111 S13: -0.0194 REMARK 3 S21: 0.0482 S22: 0.0380 S23: 0.1022 REMARK 3 S31: 0.0390 S32: -0.0550 S33: -0.0566 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 158-212) REMARK 3 ORIGIN FOR THE GROUP (A): -17.3392 20.7358 7.1922 REMARK 3 T TENSOR REMARK 3 T11: -0.1135 T22: 0.1575 REMARK 3 T33: -0.1402 T12: -0.0023 REMARK 3 T13: 0.0118 T23: -0.0048 REMARK 3 L TENSOR REMARK 3 L11: 0.6567 L22: 0.7422 REMARK 3 L33: 3.2965 L12: 0.0263 REMARK 3 L13: -0.2211 L23: 0.1585 REMARK 3 S TENSOR REMARK 3 S11: 0.0583 S12: 0.1182 S13: 0.2252 REMARK 3 S21: 0.0443 S22: -0.0432 S23: -0.0748 REMARK 3 S31: -0.2965 S32: 0.1720 S33: -0.0151 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: IDEAL-DIST CONTACT TERM CONTACT SETUP. REMARK 3 RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ADP MG TAE NO3. REMARK 3 NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=1790. NUMBER WITH APPRO REMARK 3 DEFAULT CCP4 ATOM TYPE=52. NUMBER TREATED BY BAD NON-BONDED REMARK 3 CONTACTS=1. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2XX3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-NOV-11. REMARK 100 THE PDBE ID CODE IS EBI-45824. 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 : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD (QUANTUM 315R) REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16363 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.20 REMARK 200 RESOLUTION RANGE LOW (A) : 35.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 2 REMARK 200 R MERGE (I) : 0.12 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.90 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 51.22000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.16000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.22000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.16000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 3370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.6 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 -1.000000 0.000000 0.000000 -39.92072 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 61.30841 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 A2049 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 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 ALA A 33 REMARK 465 GLY A 34 REMARK 465 SER A 55 REMARK 465 TYR A 56 REMARK 465 LEU A 57 REMARK 465 GLN A 58 REMARK 465 LYS A 59 REMARK 465 LYS A 60 REMARK 465 SER A 61 REMARK 465 ASP A 62 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 205 CG CD CE NZ 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 GLU A 64 99.99 64.96 REMARK 500 ARG A 97 140.76 77.18 REMARK 500 TYR A 98 -149.64 -143.58 REMARK 500 GLU A 110 -27.76 70.95 REMARK 500 THR A 201 -62.14 -96.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 GLU A 110 23.2 L L OUTSIDE RANGE REMARK 500 GLN A 119 25.0 L L OUTSIDE RANGE 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 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2019 O REMARK 620 2 HOH A2022 O 86.5 REMARK 620 3 ADP A 302 O2B 79.7 163.3 REMARK 620 4 HOH A2104 O 78.0 92.4 93.8 REMARK 620 5 SER A 20 OG 72.5 75.6 91.2 148.6 REMARK 620 6 HOH A2020 O 169.6 83.8 110.5 98.8 108.3 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 ADP A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TAE A1213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A1214 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1E2D RELATED DB: PDB REMARK 900 HUMAN THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE REMARK 900 MONOPHOSPHATE, 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 REMARK 900 MAGNESIUM-ION REMARK 900 RELATED ID: 1E9A RELATED DB: PDB REMARK 900 HUMAN THYMIDYLATE KINASE COMPLEXED WITH THE BISUBSTRATE REMARK 900 INHIBITOR AZTP5A REMARK 900 RELATED ID: 1E9B RELATED DB: PDB REMARK 900 HUMAN THYMIDYLATE KINASE COMPLEXED WITH AZTMP AND APPNP REMARK 900 RELATED ID: 1E98 RELATED DB: PDB REMARK 900 WILD TYPE HUMAN THYMIDYLATE KINASE COMPLEXED WITH AZTMP REMARK 900 AND ADP REMARK 900 RELATED ID: 1NN3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN THYMIDYLATE KINASE WITH D4TMP REMARK 900 +ADP REMARK 900 RELATED ID: 1E2E RELATED DB: PDB REMARK 900 HUMAN THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE REMARK 900 MONOPHOSPHATE, ADENOSINE DIPHOSPHATE,A MAGNESIUM-ION AND REMARK 900 ALF3 REMARK 900 RELATED ID: 1E9E RELATED DB: PDB REMARK 900 MUTANT HUMAN THYMIDYLATE KINASE (F105Y) COMPLEXED WITH REMARK 900 DTMP AND ADP REMARK 900 RELATED ID: 1E2Q RELATED DB: PDB REMARK 900 HUMAN THYMIDYLATE KINASE COMPLEXED WITH TP5A AND A REMARK 900 MAGNESIUM-ION REMARK 900 RELATED ID: 1E99 RELATED DB: PDB REMARK 900 HUMAN THYMIDYLATE KINASE COMPLEXED WITH AZTMP AND ADP REMARK 900 RELATED ID: 1NMX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN THYMIDYLATE KINASE WITH REMARK 900 FLTMPAND ADP REMARK 900 RELATED ID: 1NN5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN THYMIDYLATE KINASE WITH D4TMP REMARK 900 +APPNHP REMARK 900 RELATED ID: 1NMZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN THYMIDYLATE KINASE WITH REMARK 900 NH2TMPAND APPNHP REMARK 900 RELATED ID: 1NN1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN THYMIDYLATE KINASE WITH REMARK 900 DDTMPAND APPNHP REMARK 900 RELATED ID: 1E9D RELATED DB: PDB REMARK 900 MUTANT HUMAN THYMIDYLATE KINASE (F105Y) COMPLEXED WITH REMARK 900 AZTMP AND ADP REMARK 900 RELATED ID: 1NMY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN THYMIDYLATE KINASE WITH REMARK 900 FLTMPAND APPNHP REMARK 900 RELATED ID: 1E2F RELATED DB: PDB REMARK 900 HUMAN THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE REMARK 900 MONOPHOSPHATE, ADENOSINE DIPHOSPHATE AND A MAGNESIUM-ION REMARK 900 RELATED ID: 1NN0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN THYMIDYLATE KINASE WITH REMARK 900 DDTMPAND ADP REMARK 900 RELATED ID: 1E9F RELATED DB: PDB REMARK 900 MUTANT HUMAN THYMIDYLATE KINASE COMPLEXED WITH TMP AND REMARK 900 ADP REMARK 900 RELATED ID: 1E9C RELATED DB: PDB REMARK 900 MUTANT HUMAN THYMIDYLATE KINASE COMPLEXED WITH TMP AND REMARK 900 APPNP DBREF 2XX3 A 1 212 UNP P23919 KTHY_HUMAN 1 212 SEQADV 2XX3 MET A -19 UNP P23919 EXPRESSION TAG SEQADV 2XX3 GLY A -18 UNP P23919 EXPRESSION TAG SEQADV 2XX3 SER A -17 UNP P23919 EXPRESSION TAG SEQADV 2XX3 SER A -16 UNP P23919 EXPRESSION TAG SEQADV 2XX3 HIS A -15 UNP P23919 EXPRESSION TAG SEQADV 2XX3 HIS A -14 UNP P23919 EXPRESSION TAG SEQADV 2XX3 HIS A -13 UNP P23919 EXPRESSION TAG SEQADV 2XX3 HIS A -12 UNP P23919 EXPRESSION TAG SEQADV 2XX3 HIS A -11 UNP P23919 EXPRESSION TAG SEQADV 2XX3 HIS A -10 UNP P23919 EXPRESSION TAG SEQADV 2XX3 SER A -9 UNP P23919 EXPRESSION TAG SEQADV 2XX3 SER A -8 UNP P23919 EXPRESSION TAG SEQADV 2XX3 GLY A -7 UNP P23919 EXPRESSION TAG SEQADV 2XX3 LEU A -6 UNP P23919 EXPRESSION TAG SEQADV 2XX3 VAL A -5 UNP P23919 EXPRESSION TAG SEQADV 2XX3 PRO A -4 UNP P23919 EXPRESSION TAG SEQADV 2XX3 ARG A -3 UNP P23919 EXPRESSION TAG SEQADV 2XX3 GLY A -2 UNP P23919 EXPRESSION TAG SEQADV 2XX3 SER A -1 UNP P23919 EXPRESSION TAG SEQADV 2XX3 HIS A 0 UNP P23919 EXPRESSION TAG SEQRES 1 A 232 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 232 LEU VAL PRO ARG GLY SER HIS MET ALA ALA ARG ARG GLY SEQRES 3 A 232 ALA LEU ILE VAL LEU GLU GLY VAL ASP ARG ALA GLY LYS SEQRES 4 A 232 SER THR GLN SER ARG LYS LEU VAL GLU ALA LEU CYS ALA SEQRES 5 A 232 ALA GLY HIS ARG ALA GLU LEU LEU ARG PHE PRO GLU ARG SEQRES 6 A 232 SER THR GLU ILE GLY LYS LEU LEU SER SER TYR LEU GLN SEQRES 7 A 232 LYS LYS SER ASP VAL GLU ASP HIS SER VAL HIS LEU LEU SEQRES 8 A 232 PHE SER ALA ASN ARG TRP GLU GLN VAL PRO LEU ILE LYS SEQRES 9 A 232 GLU LYS LEU SER GLN GLY VAL THR LEU VAL VAL ASP ARG SEQRES 10 A 232 TYR ALA PHE SER GLY VAL ALA PHE THR GLY ALA LYS GLU SEQRES 11 A 232 ASN PHE SER LEU ASP TRP CYS LYS GLN PRO ASP VAL GLY SEQRES 12 A 232 LEU PRO LYS PRO ASP LEU VAL LEU PHE LEU GLN LEU GLN SEQRES 13 A 232 LEU ALA ASP ALA ALA LYS ARG GLY ALA PHE GLY HIS GLU SEQRES 14 A 232 ARG TYR GLU ASN GLY ALA PHE GLN GLU ARG ALA LEU ARG SEQRES 15 A 232 CYS PHE HIS GLN LEU MET LYS ASP THR THR LEU ASN TRP SEQRES 16 A 232 LYS MET VAL ASP ALA SER LYS SER ILE GLU ALA VAL HIS SEQRES 17 A 232 GLU ASP ILE ARG VAL LEU SER GLU ASP ALA ILE ARG THR SEQRES 18 A 232 ALA THR GLU LYS PRO LEU GLY GLU LEU TRP LYS HET ADP A 302 27 HET MG A 401 1 HET TAE A1213 21 HET NO3 A1214 4 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM TAE N1-[(E)-4-DIHYDROXYPHOSPHONYL-BUT-2-ENYL]- HETNAM 2 TAE THYMINE HETNAM NO3 NITRATE ION FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 MG MG 2+ FORMUL 4 TAE C9 H14 N2 O8 P2 FORMUL 5 NO3 N O3 1- FORMUL 6 HOH *203(H2 O) HELIX 1 1 GLY A 18 ALA A 32 1 15 HELIX 2 2 THR A 47 LEU A 53 1 7 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 LYS A 109 1 12 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 HIS A 148 GLU A 152 5 5 HELIX 10 10 ASN A 153 MET A 168 1 16 HELIX 11 11 SER A 183 THR A 201 1 19 HELIX 12 12 ALA A 202 LYS A 205 5 4 SHEET 1 AA 5 ALA A 37 ARG A 41 0 SHEET 2 AA 5 THR A 92 ASP A 96 1 O THR A 92 N GLU A 38 SHEET 3 AA 5 LEU A 8 GLU A 12 1 O ILE A 9 N VAL A 95 SHEET 4 AA 5 LEU A 129 GLN A 134 1 O LEU A 129 N VAL A 10 SHEET 5 AA 5 TRP A 175 ASP A 179 1 O LYS A 176 N PHE A 132 LINK O2B ADP A 302 MG MG A 401 1555 1555 2.07 LINK MG MG A 401 O HOH A2020 1555 1555 1.95 LINK MG MG A 401 O HOH A2022 1555 1555 1.95 LINK MG MG A 401 O HOH A2104 1555 1555 2.05 LINK MG MG A 401 OG SER A 20 1555 1555 2.43 LINK MG MG A 401 O HOH A2019 1555 1555 2.30 CISPEP 1 PHE A 42 PRO A 43 0 2.77 SITE 1 AC1 23 ARG A 16 ALA A 17 GLY A 18 LYS A 19 SITE 2 AC1 23 SER A 20 THR A 21 ARG A 143 GLY A 144 SITE 3 AC1 23 ALA A 145 MET A 177 VAL A 178 ASP A 179 SITE 4 AC1 23 LYS A 182 ILE A 184 MG A 401 HOH A2019 SITE 5 AC1 23 HOH A2027 HOH A2104 HOH A2125 HOH A2141 SITE 6 AC1 23 HOH A2146 HOH A2174 HOH A2202 SITE 1 AC2 6 SER A 20 ADP A 302 HOH A2019 HOH A2020 SITE 2 AC2 6 HOH A2022 HOH A2104 SITE 1 AC3 13 PHE A 42 ARG A 45 PHE A 72 ARG A 76 SITE 2 AC3 13 ARG A 97 GLY A 102 PHE A 105 HIS A 148 SITE 3 AC3 13 ARG A 150 TYR A 151 HOH A2022 HOH A2084 SITE 4 AC3 13 HOH A2143 SITE 1 AC4 7 LYS A 25 GLN A 134 LEU A 161 HIS A 165 SITE 2 AC4 7 ILE A 184 HOH A2126 HOH A2129 CRYST1 102.440 38.320 73.160 90.00 123.07 90.00 C 1 2 1 4 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 0.009762 0.000000 0.006356 0.00000 SCALE2 0.000000 0.026096 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016311 0.00000