3QES Transferase Dna date Jan 20, 2011
title Rb69 Dna Polymerase (L561as565gy567a) Ternary Complex With Opposite Difluorotoluene Nucleoside
authors S.Xia, W.H.Konigsberg, J.Wang
compound source
Molecule: Dna Polymerase
Chain: A
Engineered: Yes
Mutation: Yes
Organism_scientific: Enterobacteria Phage Rb69
Organism_common: Bacteriophage Rb69
Organism_taxid: 12353
Gene: 43
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Psp72

Molecule: Dna (5'-D(Tpcpgp(Dft) Pgptpapapgpcpapgptpcpcpgpcpg)-3');
Chain: T
Engineered: Yes
Other_details: Dna Template

Synthetic: Yes

Molecule: Dna (5'-D(Gpcpgpgpapcptpgpcptptpap(D
Chain: P
Engineered: Yes
Other_details: Dna Primer

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.177 R_Free 0.218
length a length b length c angle alpha angle beta angle gamma
74.824 119.979 130.068 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.98 Å
ligand CA, DFT, DGT, DOC enzyme Transferase E.C. BRENDA
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity

  • Primary referenceStructural Basis for Differential Insertion Kinetics of dNMPs Opposite a Difluorotoluene Nucleotide Residue., Xia S, Eom SH, Konigsberg WH, Wang J, Biochemistry. 2012 Feb 21;51(7):1476-85. Epub 2012 Feb 8. PMID:22304682
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (372 Kb) [Save to disk]
  • Biological Unit Coordinates (3qes.pdb1.gz) 365 Kb
  • LPC: Ligand-Protein Contacts for 3QES
  • CSU: Contacts of Structural Units for 3QES
  • Structure Factors (961 Kb)
  • Retrieve 3QES in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3QES from S2C, [Save to disk]
  • Re-refined 3qes structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3QES 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 3QES
  • 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 3QES, from MSDmotif at EBI
  • Fold representative 3qes from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3qes] [3qes_A] [3qes_P] [3qes_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3QES: [POLBc ] by SMART
  • Other resources with information on 3QES
  • Community annotation for 3QES at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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