1TK8 T7 DNA polymerase ternary complex with 8 oxo guanosine and dAMP at the elongation site date
authors Brieba, L.G., Eichman, B.F., Kokoska, R.J., Doublie, S., Kunkel, T.A., Ellenberger, T.
compound source
symmetry
R_factor
R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.50
ligand 1PE, 2DA, 8OG, D3T, MES, MG, SO4 enzyme
related structures by homologous chain: 1T8E, 1TKD
Gene
Ontology
ChainFunctionProcessComponent
A
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity


    • B
  • DNA polymerase processivity ...


    • Primary referenceStructural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase., Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T, EMBO J 2004 Sep 1;23(17):3452-61. Epub 2004 Aug 5. PMID:15297882
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (163 Kb) [Save to disk]
  • Biological Unit Coordinates (1tk8.pdb1.gz) 156 Kb
  • LPC: Ligand-Protein Contacts for 1TK8
  • CSU: Contacts of Structural Units for 1TK8
  • Likely Quarternary Molecular Structure file(s) for 1TK8
  • Structure Factors (537 Kb)
  • Retrieve 1TK8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1TK8 from S2C, [Save to disk]
  • Re-refined 1tk8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1TK8 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 1TK8
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1TK8, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1tk8a1, region A:1-210 [Jmol] [rasmolscript] [script source]
        - Domain d1tk8a2, region A:211-704 [Jmol] [rasmolscript] [script source]
        - Domain d1tk8b_, region B [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1tk8] [1tk8_A] [1tk8_P] [1tk8_B] [1tk8_T]
  • SWISS-PROT database: [P00581] [P0AA25]
  • Domain organization of [DPOL_BPT7] [THIO_ECOLI] by SWISSPFAM
  • Domain found in 1TK8: [POLAc ] by SMART
    • Other resources with information on 1TK8
  • Community annotation for 1TK8 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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