1TKD Transferase Electron Transport Dna date Jun 08, 2004
title T7 Dna Polymerase Ternary Complex With 8 Oxo Guanosine And D Elongation Site
authors L.G.Brieba, B.F.Eichman, R.J.Kokoska, S.Doublie, T.A.Kunkel, T.El
compound source
Molecule: Dna (5'- D(Cpgpapapapapcpgpapcpgpgpcpcpapgptpgpcp C))-3');
Chain: P
Engineered: Yes
 Synthetic: Yes

Molecule: Dna (5'-D(Cpcpcpap(8og) Ptpgpgpcpapcptpgpgpcpcpgptpcpgptptptptp
Chain: T
Engineered: Yes
Synthetic: Yes

Molecule: Dna Polymerase
Chain: A
Synonym: T7 Dna Polymerase
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Enterobacteria Phage T7
Organism_taxid: 10760
Gene: 5
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_plasmid: Pgp5

Molecule: Thioredoxin 1
Chain: B
Synonym: Trx1, Trx
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Trxa, Tsnc, Fipa, B3781, C4701, Z5291, Ecs4714, Stm39 Stmd1.75, Sty3639, T3381, Sf3854, S3905;
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_plasmid: Ptrx-3
symmetry Space Group: P 21 21 2
R_factor 0.202 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.514 215.112 52.035 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.49 Å
ligand 1PE, 8OG, D3T, DOC, MES, MG, SO4 enzyme Transferase E.C.2.7.7.7 BRENDA
related structures by homologous chain: 1SKR, 1TK8
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] (164 Kb) [Save to disk]
  • Biological Unit Coordinates (1tkd.pdb1.gz) 157 Kb
  • LPC: Ligand-Protein Contacts for 1TKD
  • CSU: Contacts of Structural Units for 1TKD
  • Likely Quarternary Molecular Structure file(s) for 1TKD
  • Structure Factors (423 Kb)
  • Retrieve 1TKD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1TKD from S2C, [Save to disk]
  • Re-refined 1tkd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1TKD 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 1TKD
  • 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 1TKD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1tkda1, region A:1-210 [Jmol] [rasmolscript] [script source]
        - Domain d1tkda2, region A:211-704 [Jmol] [rasmolscript] [script source]
        - Domain d1tkdb_, 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: [1tkd_A] [1tkd_B] [1tkd_T] [1tkd_P] [1tkd]
  • SWISS-PROT database: [P00581] [P0AA25]
  • Domain organization of [DPOL_BPT7] [THIO_ECOLI] by SWISSPFAM
  • Domain found in 1TKD: [POLAc ] by SMART
    • Other resources with information on 1TKD
  • Community annotation for 1TKD 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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