4UB5 DNA polymerase beta substrate complex with a templating cytosine, incoming 8-oxodGTP, and Mn2+, 5 s date
authors Freudenthal, B.D., Wilson, S.H., Beard, W.A.
compound source
symmetry
R_factor
R_Free 0.2895
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.15
ligand 8DG, MN, NA enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceUncovering the polymerase-induced cytotoxicity of an oxidized nucleotide., Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH, Nature. 2014 Nov 17. doi: 10.1038/nature13886. PMID:25409153
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (4ub5.pdb1.gz) 67 Kb
  • LPC: Ligand-Protein Contacts for 4UB5
  • CSU: Contacts of Structural Units for 4UB5
  • Structure Factors (370 Kb)
  • Retrieve 4UB5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4UB5 from S2C, [Save to disk]
  • Re-refined 4ub5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4UB5 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 4UB5
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4UB5, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ub5_P] [4ub5_D] [4ub5_T] [4ub5] [4ub5_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4UB5: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4UB5
  • Community annotation for 4UB5 at PDBWiki (http://pdbwiki.org)

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