4m3w Summary

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RB69 DNA polymerase ternary complex with dT/dG at position n-4 of primer/template duplex

The structure was published by Xia, S. and Konigsberg, W.H., in 2014 in a paper entitled "Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.1 Å and deposited in 2013.

The experimental data on which the structure is based was also deposited.

This PDB entry contains a complex of 3 biomacromolecules, namely DNA polymerase, DNA template, and DNA primer.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule most likely forms heterotrimers.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A DNA polymerase Q38087 (1-903) (DPOL_BPR69)search Enterobacteria phage RB69search 99% 903 100%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
Q38087 (1 - 903) DNA polymerase Enterobacteria phage RB69

Chain Sequence family (Pfam)
A (Q38087) PF00136: DNA polymerase family Bsearch, PF03104: DNA polymerase family B, exonuclease domainsearch

Chain ID Molecular function (GO) Biological process (GO)
A (Q38087) nucleic acid bindingsearch nucleotide bindingsearch 3'-5' exonuclease activitysearch DNA bindingsearch DNA-directed DNA polymerase activitysearch nucleotidyltransferase activitysearch hydrolase activitysearch transferase activitysearch exonuclease activitysearch nuclease activitysearch nucleic acid phosphodiester bond hydrolysissearch DNA replicationsearch DNA biosynthetic processsearch viral DNA genome replicationsearch

Chain InterPro annotation
A DNA-directed DNA polymerase, family B, exonuclease domainsearch DNA-directed DNA polymerase, family B, multifunctional domainsearch DNA-directed DNA polymerase, family Bsearch Ribonuclease H-like domainsearch DNA-directed DNA polymerase, family B, conserved sitesearch DNA polymerase, palm domainsearch