4UB1 DNA polymerase beta product complex with a templating adenine and 8-oxodGMP, 90 s date
authors Freudenthal, B.D., Wilson, S.H., Beard, W.A.
compound source
symmetry
R_factor
R_Free 0.2772
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.34
ligand 8OG, 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] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (4ub1.pdb1.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 4UB1
  • CSU: Contacts of Structural Units for 4UB1
  • Structure Factors (234 Kb)
  • Retrieve 4UB1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4UB1 from S2C, [Save to disk]
  • Re-refined 4ub1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4UB1 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 4UB1
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4UB1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1o4ub1, region B:104-273 [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ub1_P] [4ub1_D] [4ub1_T] [4ub1] [4ub1_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4UB1: [HhH1] [POLXc ] by SMART
    • Other resources with information on 4UB1
  • Community annotation for 4UB1 at PDBWiki (http://pdbwiki.org)

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