5VU7 Transferase Dna date May 18, 2017
title Tna Polymerase, Open Ternary Complex
authors N.Chim, J.C.Chaput
compound source
Molecule: Dna Polymerase
Chain: A
Synonym: Kod-Ri
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Thermococcus Kodakarensis
Organism_taxid: 311400
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Template
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dnatna Hybrid Primer
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 2 21 21
R_factor 0.214 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.550 112.610 145.460 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.72 Å
ligand
enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...


  • Primary referenceStructural basis for TNA synthesis by an engineered TNA polymerase., Chim N, Shi C, Sau SP, Nikoomanzar A, Chaput JC, Nat Commun. 2017 Nov 27;8(1):1810. doi: 10.1038/s41467-017-02014-0. PMID:29180809
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (289 Kb) [Save to disk]
  • Biological Unit Coordinates (5vu7.pdb1.gz) 283 Kb
  • CSU: Contacts of Structural Units for 5VU7
  • Structure Factors (283 Kb)
  • Retrieve 5VU7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VU7 from S2C, [Save to disk]
  • View 5VU7 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 5VU7
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5vu7 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vu7_A] [5vu7_P] [5vu7_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VU7
  • Community annotation for 5VU7 at PDBWiki (http://pdbwiki.org)

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