HEADER TRANSFERASE/DNA 13-NOV-01 1KDH TITLE BINARY COMPLEX OF MURINE TERMINAL DEOXYNUCLEOTIDYL TRANSFERASE WITH A TITLE 2 PRIMER SINGLE STRANDED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(P*(BRU)P*(BRU)P*(BRU)P*(BRU))-3'; COMPND 3 CHAIN: D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE SHORT ISOFORM; COMPND 7 CHAIN: A; COMPND 8 EC: 2.7.7.31; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 5 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 6 ORGANISM_TAXID: 10090; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS POLYMERASE, NUCLEOTIDYL TRANSFERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.DELARUE,J.B.BOULE,J.LESCAR,N.EXPERT-BEZANCON,N.JOURDAN,N.SUKUMAR, AUTHOR 2 F.ROUGEON,C.PAPANICOLAOU REVDAT 4 16-AUG-23 1KDH 1 REMARK LINK REVDAT 3 20-NOV-19 1KDH 1 LINK REVDAT 2 24-FEB-09 1KDH 1 VERSN REVDAT 1 13-MAY-02 1KDH 0 JRNL AUTH M.DELARUE,J.B.BOULE,J.LESCAR,N.EXPERT-BEZANCON,N.JOURDAN, JRNL AUTH 2 N.SUKUMAR,F.ROUGEON,C.PAPANICOLAOU JRNL TITL CRYSTAL STRUCTURES OF A TEMPLATE-INDEPENDENT DNA POLYMERASE: JRNL TITL 2 MURINE TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE. JRNL REF EMBO J. V. 21 427 2002 JRNL REFN ISSN 0261-4189 JRNL PMID 11823435 JRNL DOI 10.1093/EMBOJ/21.3.427 REMARK 2 REMARK 2 RESOLUTION. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 8579 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) : 0.239 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 405 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 2846 REMARK 3 NUCLEIC ACID ATOMS : 81 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 1 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) : 4.21800 REMARK 3 B22 (A**2) : 12.74700 REMARK 3 B33 (A**2) : -16.94000 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.380 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.437 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.579 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.874 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.107 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CIS_PEPTIDE.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : DNA-RNA.PARAM REMARK 3 PARAMETER FILE 5 : ION.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KDH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1000014837. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-SEP-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.960 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8579 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 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 (%) : 91.5 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : 0.07500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.60800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 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 1JMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6K, 1M LICL, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.40000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.70000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.70000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.40000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.50000 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 APPLY THE FOLLOWING TO CHAINS: D, 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 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 LYS A 394 REMARK 465 VAL A 395 REMARK 465 ASP A 396 REMARK 465 ALA A 397 REMARK 465 GLY A 421 REMARK 465 GLN A 422 REMARK 465 GLN A 423 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 148 CG CD CE NZ REMARK 470 LYS A 149 CG CD CE NZ REMARK 470 GLU A 212 CG CD OE1 OE2 REMARK 470 LYS A 238 CG CD CE NZ REMARK 470 LYS A 387 CG CD CE NZ REMARK 470 ARG A 393 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 398 CG CD1 CD2 REMARK 470 GLU A 418 CG CD OE1 OE2 REMARK 470 LYS A 419 CG CD CE NZ REMARK 470 SER A 420 OG REMARK 470 GLU A 424 CG CD OE1 OE2 REMARK 470 LYS A 426 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TRP A 428 NE1 TRP A 428 CE2 0.113 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 PRO A 202 C - N - CA ANGL. DEV. = 9.4 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 LYS A 149 81.94 50.11 REMARK 500 SER A 151 156.41 -45.46 REMARK 500 THR A 160 -157.75 -79.90 REMARK 500 ASN A 162 72.49 -105.74 REMARK 500 ASN A 184 74.61 -114.26 REMARK 500 GLU A 212 67.13 -67.54 REMARK 500 GLU A 230 -85.57 -83.65 REMARK 500 SER A 254 0.12 -66.68 REMARK 500 LYS A 261 -78.99 -49.83 REMARK 500 ASP A 280 107.78 -43.08 REMARK 500 SER A 282 -58.66 -162.87 REMARK 500 LEU A 323 74.50 -157.02 REMARK 500 PRO A 324 -5.61 -57.34 REMARK 500 THR A 331 -166.47 -109.07 REMARK 500 ALA A 353 130.91 -36.54 REMARK 500 GLN A 359 -74.13 -88.04 REMARK 500 ASP A 399 76.72 48.04 REMARK 500 GLN A 402 99.39 -63.32 REMARK 500 CYS A 404 104.74 -166.78 REMARK 500 THR A 465 -73.36 -66.78 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 NA A 2 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BRU D 2 OP1 REMARK 620 2 THR A 253 O 151.3 REMARK 620 3 VAL A 255 O 77.3 76.4 REMARK 620 4 VAL A 258 O 82.5 86.0 89.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 1 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BRU D 3 O3' REMARK 620 2 ASP A 434 OD2 156.0 REMARK 620 N 1 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 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JMS RELATED DB: PDB REMARK 900 UNLIGANDED MURINE TERMINAL DEOXYNUCLEOTIDYL TRANSFERASE REMARK 900 RELATED ID: 1BPY RELATED DB: PDB REMARK 900 TERNARY COMPLEX OF HUMAN POLYMERASE BETA REMARK 900 RELATED ID: 1KEJ RELATED DB: PDB REMARK 900 TDT COMPLEXED WITH DDATP DBREF 1KDH A 148 510 GB 12802443 AAK07885 148 510 DBREF 1KDH D 1 4 PDB 1KDH 1KDH 1 4 SEQRES 1 D 4 BRU BRU BRU BRU SEQRES 1 A 363 LYS LYS ILE SER GLN TYR ALA CYS GLN ARG ARG THR THR SEQRES 2 A 363 LEU ASN ASN TYR ASN GLN LEU PHE THR ASP ALA LEU ASP SEQRES 3 A 363 ILE LEU ALA GLU ASN ASP GLU LEU ARG GLU ASN GLU GLY SEQRES 4 A 363 SER CYS LEU ALA PHE MET ARG ALA SER SER VAL LEU LYS SEQRES 5 A 363 SER LEU PRO PHE PRO ILE THR SER MET LYS ASP THR GLU SEQRES 6 A 363 GLY ILE PRO CYS LEU GLY ASP LYS VAL LYS SER ILE ILE SEQRES 7 A 363 GLU GLY ILE ILE GLU ASP GLY GLU SER SER GLU ALA LYS SEQRES 8 A 363 ALA VAL LEU ASN ASP GLU ARG TYR LYS SER PHE LYS LEU SEQRES 9 A 363 PHE THR SER VAL PHE GLY VAL GLY LEU LYS THR ALA GLU SEQRES 10 A 363 LYS TRP PHE ARG MET GLY PHE ARG THR LEU SER LYS ILE SEQRES 11 A 363 GLN SER ASP LYS SER LEU ARG PHE THR GLN MET GLN LYS SEQRES 12 A 363 ALA GLY PHE LEU TYR TYR GLU ASP LEU VAL SER CYS VAL SEQRES 13 A 363 ASN ARG PRO GLU ALA GLU ALA VAL SER MET LEU VAL LYS SEQRES 14 A 363 GLU ALA VAL VAL THR PHE LEU PRO ASP ALA LEU VAL THR SEQRES 15 A 363 MET THR GLY GLY PHE ARG ARG GLY LYS MET THR GLY HIS SEQRES 16 A 363 ASP VAL ASP PHE LEU ILE THR SER PRO GLU ALA THR GLU SEQRES 17 A 363 ASP GLU GLU GLN GLN LEU LEU HIS LYS VAL THR ASP PHE SEQRES 18 A 363 TRP LYS GLN GLN GLY LEU LEU LEU TYR CYS ASP ILE LEU SEQRES 19 A 363 GLU SER THR PHE GLU LYS PHE LYS GLN PRO SER ARG LYS SEQRES 20 A 363 VAL ASP ALA LEU ASP HIS PHE GLN LYS CYS PHE LEU ILE SEQRES 21 A 363 LEU LYS LEU ASP HIS GLY ARG VAL HIS SER GLU LYS SER SEQRES 22 A 363 GLY GLN GLN GLU GLY LYS GLY TRP LYS ALA ILE ARG VAL SEQRES 23 A 363 ASP LEU VAL MET CYS PRO TYR ASP ARG ARG ALA PHE ALA SEQRES 24 A 363 LEU LEU GLY TRP THR GLY SER ARG GLN PHE GLU ARG ASP SEQRES 25 A 363 LEU ARG ARG TYR ALA THR HIS GLU ARG LYS MET MET LEU SEQRES 26 A 363 ASP ASN HIS ALA LEU TYR ASP ARG THR LYS ARG VAL PHE SEQRES 27 A 363 LEU GLU ALA GLU SER GLU GLU GLU ILE PHE ALA HIS LEU SEQRES 28 A 363 GLY LEU ASP TYR ILE GLU PRO TRP GLU ARG ASN ALA MODRES 1KDH BRU D 1 DU MODRES 1KDH BRU D 2 DU MODRES 1KDH BRU D 3 DU MODRES 1KDH BRU D 4 DU HET BRU D 1 21 HET BRU D 2 20 HET BRU D 3 20 HET BRU D 4 20 HET MG A 1 1 HET NA A 2 1 HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION FORMUL 1 BRU 4(C9 H12 BR N2 O8 P) FORMUL 3 MG MG 2+ FORMUL 4 NA NA 1+ FORMUL 5 HOH *(H2 O) HELIX 1 1 TYR A 153 ARG A 157 5 5 HELIX 2 2 ASN A 165 ARG A 182 1 18 HELIX 3 3 ASN A 184 SER A 200 1 17 HELIX 4 4 SER A 207 GLU A 212 5 6 HELIX 5 5 GLY A 218 GLY A 232 1 15 HELIX 6 6 SER A 234 ASP A 243 1 10 HELIX 7 7 ASP A 243 SER A 254 1 12 HELIX 8 8 GLY A 259 MET A 269 1 11 HELIX 9 9 THR A 273 ASP A 280 1 8 HELIX 10 10 THR A 286 TYR A 295 1 10 HELIX 11 11 TYR A 295 SER A 301 1 7 HELIX 12 12 ASN A 304 LEU A 323 1 20 HELIX 13 13 GLY A 333 GLY A 337 5 5 HELIX 14 14 THR A 354 GLN A 371 1 18 HELIX 15 15 GLY A 413 VAL A 415 5 3 HELIX 16 16 ARG A 442 THR A 451 1 10 HELIX 17 17 SER A 453 LYS A 469 1 17 HELIX 18 18 SER A 490 GLY A 499 1 10 HELIX 19 19 GLU A 504 ARG A 508 5 5 SHEET 1 A 5 LEU A 327 THR A 331 0 SHEET 2 A 5 ASP A 343 SER A 350 -1 O THR A 349 N LEU A 327 SHEET 3 A 5 TRP A 428 PRO A 439 1 O VAL A 436 N ILE A 348 SHEET 4 A 5 LYS A 403 ASP A 411 -1 N LEU A 408 O ILE A 431 SHEET 5 A 5 LEU A 375 ASP A 379 -1 N ASP A 379 O PHE A 405 SHEET 1 B 3 MET A 470 LEU A 472 0 SHEET 2 B 3 LEU A 477 ASP A 479 -1 O TYR A 478 N MET A 471 SHEET 3 B 3 VAL A 484 LEU A 486 -1 O LEU A 486 N LEU A 477 LINK O3' BRU D 1 P BRU D 2 1555 1555 1.61 LINK O3' BRU D 2 P BRU D 3 1555 1555 1.61 LINK O3' BRU D 3 P BRU D 4 1555 1555 1.61 LINK OP1 BRU D 2 NA NA A 2 1555 1555 2.43 LINK O3' BRU D 3 MG MG A 1 1555 1555 2.82 LINK MG MG A 1 OD2 ASP A 434 1555 1555 1.89 LINK NA NA A 2 O THR A 253 1555 1555 2.40 LINK NA NA A 2 O VAL A 255 1555 1555 3.12 LINK NA NA A 2 O VAL A 258 1555 1555 2.34 CISPEP 1 GLY A 452 SER A 453 0 -1.13 SITE 1 AC1 6 ASP A 343 ASP A 345 ASP A 434 TRP A 450 SITE 2 AC1 6 BRU D 3 BRU D 4 SITE 1 AC2 4 THR A 253 VAL A 255 VAL A 258 BRU D 2 CRYST1 46.800 85.000 111.400 90.00 90.00 90.00 P 21 21 21 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 0.021368 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011765 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008977 0.00000 HETATM 1 N1 BRU D 1 30.991 62.423 77.937 1.00 93.44 N HETATM 2 C2 BRU D 1 29.692 62.000 78.207 1.00 94.34 C HETATM 3 N3 BRU D 1 28.801 62.167 77.174 1.00 96.40 N HETATM 4 C4 BRU D 1 29.052 62.698 75.921 1.00 98.55 C HETATM 5 C5 BRU D 1 30.410 63.114 75.703 1.00 99.51 C HETATM 6 C6 BRU D 1 31.307 62.983 76.702 1.00 97.63 C HETATM 7 O2 BRU D 1 29.353 61.516 79.279 1.00 92.19 O HETATM 8 O4 BRU D 1 28.114 62.851 75.135 1.00 98.47 O HETATM 9 BR BRU D 1 30.990 63.773 73.905 1.00104.07 BR HETATM 10 C1' BRU D 1 32.007 62.237 78.996 1.00 88.95 C HETATM 11 C2' BRU D 1 33.461 62.424 78.568 1.00 85.46 C HETATM 12 C3' BRU D 1 34.125 62.973 79.820 1.00 82.83 C HETATM 13 C4' BRU D 1 33.009 63.755 80.514 1.00 82.94 C HETATM 14 O3' BRU D 1 34.563 61.916 80.662 1.00 81.73 O HETATM 15 O4' BRU D 1 31.764 63.200 80.021 1.00 85.39 O HETATM 16 C5' BRU D 1 33.036 65.235 80.216 1.00 81.33 C HETATM 17 O5' BRU D 1 32.953 65.439 78.794 1.00 78.15 O HETATM 18 P BRU D 1 33.170 66.905 78.127 1.00 76.14 P HETATM 19 OP1 BRU D 1 34.549 67.376 78.562 1.00 75.64 O HETATM 20 OP2 BRU D 1 32.032 67.767 78.656 1.00 76.45 O HETATM 21 OP3 BRU D 1 33.069 66.641 76.630 1.00 76.60 O HETATM 22 N1 BRU D 2 32.204 58.059 78.403 1.00 90.18 N HETATM 23 C2 BRU D 2 30.867 57.895 78.725 1.00 91.09 C HETATM 24 N3 BRU D 2 29.988 58.486 77.853 1.00 91.94 N HETATM 25 C4 BRU D 2 30.302 59.218 76.730 1.00 93.00 C HETATM 26 C5 BRU D 2 31.705 59.359 76.487 1.00 93.47 C HETATM 27 C6 BRU D 2 32.575 58.793 77.309 1.00 92.32 C HETATM 28 O2 BRU D 2 30.486 57.283 79.710 1.00 90.11 O HETATM 29 O4 BRU D 2 29.394 59.683 76.039 1.00 92.00 O HETATM 30 BR BRU D 2 32.359 60.338 74.865 1.00 97.94 BR HETATM 31 C1' BRU D 2 33.219 57.409 79.249 1.00 88.24 C HETATM 32 C2' BRU D 2 34.653 57.688 78.840 1.00 87.06 C HETATM 33 C3' BRU D 2 35.390 57.468 80.146 1.00 85.95 C HETATM 34 C4' BRU D 2 34.404 57.977 81.202 1.00 85.56 C HETATM 35 O3' BRU D 2 35.670 56.075 80.339 1.00 85.26 O HETATM 36 O4' BRU D 2 33.094 57.905 80.580 1.00 86.53 O HETATM 37 C5' BRU D 2 34.638 59.396 81.676 1.00 83.94 C HETATM 38 O5' BRU D 2 35.911 59.886 81.220 1.00 81.91 O HETATM 39 P BRU D 2 36.026 61.287 80.463 1.00 80.79 P HETATM 40 OP1 BRU D 2 37.005 62.120 81.207 1.00 81.84 O HETATM 41 OP2 BRU D 2 36.229 61.040 79.012 1.00 81.11 O HETATM 42 N1 BRU D 3 33.340 54.145 75.197 1.00 98.39 N HETATM 43 C2 BRU D 3 32.206 54.245 74.408 1.00100.07 C HETATM 44 N3 BRU D 3 32.001 55.488 73.855 1.00101.89 N HETATM 45 C4 BRU D 3 32.796 56.611 74.010 1.00103.58 C HETATM 46 C5 BRU D 3 33.933 56.417 74.874 1.00104.22 C HETATM 47 C6 BRU D 3 34.142 55.235 75.423 1.00102.10 C HETATM 48 O2 BRU D 3 31.441 53.311 74.214 1.00 99.76 O HETATM 49 O4 BRU D 3 32.523 57.632 73.376 1.00103.73 O HETATM 50 BR BRU D 3 35.236 57.904 75.186 1.00110.45 BR HETATM 51 C1' BRU D 3 33.702 52.841 75.773 1.00 94.49 C HETATM 52 C2' BRU D 3 35.214 52.733 75.963 1.00 92.62 C HETATM 53 C3' BRU D 3 35.400 52.132 77.339 1.00 90.49 C HETATM 54 C4' BRU D 3 34.089 52.431 78.067 1.00 89.63 C HETATM 55 O3' BRU D 3 35.716 50.744 77.241 1.00 89.42 O HETATM 56 O4' BRU D 3 33.106 52.753 77.057 1.00 90.64 O HETATM 57 C5' BRU D 3 34.201 53.612 79.003 1.00 87.79 C HETATM 58 O5' BRU D 3 34.976 54.652 78.399 1.00 84.98 O HETATM 59 P BRU D 3 36.277 55.210 79.128 1.00 84.35 P HETATM 60 OP1 BRU D 3 37.011 54.070 79.735 1.00 84.67 O HETATM 61 OP2 BRU D 3 36.982 56.115 78.182 1.00 84.70 O HETATM 62 N1 BRU D 4 36.246 49.353 72.282 1.00 93.82 N HETATM 63 C2 BRU D 4 35.938 49.721 70.978 1.00 95.10 C HETATM 64 N3 BRU D 4 34.610 49.979 70.745 1.00 95.11 N HETATM 65 C4 BRU D 4 33.583 49.904 71.650 1.00 95.37 C HETATM 66 C5 BRU D 4 33.983 49.517 72.966 1.00 95.69 C HETATM 67 C6 BRU D 4 35.265 49.271 73.233 1.00 94.59 C HETATM 68 O2 BRU D 4 36.775 49.810 70.095 1.00 96.42 O HETATM 69 O4 BRU D 4 32.440 50.201 71.297 1.00 95.15 O HETATM 70 BR BRU D 4 32.622 49.383 74.416 1.00 96.73 BR HETATM 71 C1' BRU D 4 37.649 49.040 72.602 1.00 91.77 C HETATM 72 C2' BRU D 4 38.424 50.135 73.323 1.00 89.83 C HETATM 73 C3' BRU D 4 39.471 49.328 74.073 1.00 88.53 C HETATM 74 C4' BRU D 4 38.707 48.055 74.456 1.00 88.43 C HETATM 75 O3' BRU D 4 40.558 49.071 73.152 1.00 84.47 O HETATM 76 O4' BRU D 4 37.665 47.907 73.463 1.00 89.51 O HETATM 77 C5' BRU D 4 38.063 48.055 75.826 1.00 88.29 C HETATM 78 O5' BRU D 4 37.070 49.079 75.919 1.00 87.29 O HETATM 79 P BRU D 4 37.238 50.305 76.930 1.00 88.43 P HETATM 80 OP1 BRU D 4 37.856 49.829 78.196 1.00 87.58 O HETATM 81 OP2 BRU D 4 37.881 51.427 76.186 1.00 87.05 O TER 82 BRU D 4