4j2e Summary

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RB69 DNA Polymerase L415M Ternary Complex

The structure was published by Xia, S., Wood, M., Bradley, M.J., De La Cruz, E.M., and Konigsberg, W.H., in 2013 in a paper entitled "Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.02 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 (5'-D(*TP*CP*GP*TP*CP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'), and DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*G)-3').

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 (1-901) (DPOL_BPR69)search Enterobacteria phage RB69search 99% 901 100%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
Q38087 (1 - 901) 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) nuclease activitysearch transferase activitysearch DNA bindingsearch DNA-directed DNA polymerase activitysearch nucleic acid bindingsearch nucleotide bindingsearch nucleotidyltransferase activitysearch hydrolase activitysearch exonuclease activitysearch DNA biosynthetic processsearch nucleic acid phosphodiester bond hydrolysissearch DNA replicationsearch nucleobase-containing compound metabolic processsearch

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