3SPY Transferase Dna date Jul 04, 2011
title Rb69 Dna Polymerase(L415al561as565gy567a) Ternary Complex Dupcpp Opposite Da
authors S.Xia, W.H.Konigsberg, J.Wang
compound source
Molecule: Dna Polymerase
Chain: A
Synonym: Gp43
Engineered: Yes
Mutation: Yes
Organism_scientific: Enterobacteria Phage Rb69
Organism_taxid: 12353
Gene: 43
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 5'-D(Tpcpgpapgptpapapgpcpapgptpcpc -3';
Chain: T
Engineered: Yes
Other_details: Template

Synthetic: Yes

Molecule: 5'-D(Gpcpgpgpapcptpgpcptptpapc)-3'
Chain: P
Engineered: Yes
Other_details: Primer

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.191 R_Free 0.242
length a length b length c angle alpha angle beta angle gamma
75.336 120.598 130.812 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.14 Å
ligand MG, UPC enzyme Transferase E.C. BRENDA
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity

  • Primary referenceStructural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase., Xia S, Wang M, Blaha G, Konigsberg WH, Wang J, Biochemistry. 2011 Oct 25;50(42):9114-24. Epub 2011 Sep 29. PMID:21923197
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (344 Kb) [Save to disk]
  • Biological Unit Coordinates (3spy.pdb1.gz) 337 Kb
  • LPC: Ligand-Protein Contacts for 3SPY
  • CSU: Contacts of Structural Units for 3SPY
  • Structure Factors (789 Kb)
  • Retrieve 3SPY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3SPY from S2C, [Save to disk]
  • Re-refined 3spy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3SPY 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 3SPY
  • 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
  • 3D motif for 3SPY, from MSDmotif at EBI
  • Fold representative 3spy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3spy_A] [3spy_P] [3spy_T] [3spy]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3SPY: [POLBc ] by SMART
  • Other resources with information on 3SPY
  • Community annotation for 3SPY at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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