4RPY Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine(8-oxoG) and dCTP soaked with MgCl2 for 30 s date
authors Vyas, R., Suo, Z.
compound source
symmetry
R_factor
R_Free 0.22982
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.90
ligand 8OG, ACT, CL, DCP, MG, NA, PPV enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceViewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography., Vyas R, Reed AJ, Tokarsky EJ, Suo Z, J Am Chem Soc. 2015 Apr 9. PMID:25825995
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk]
  • Biological Unit Coordinates (4rpy.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 4RPY
  • CSU: Contacts of Structural Units for 4RPY
  • Structure Factors (1774 Kb)
  • Retrieve 4RPY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4RPY from S2C, [Save to disk]
  • Re-refined 4rpy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4RPY 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 4RPY
  • 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
  • 3D motif for 4RPY, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4rpy] [4rpy_A] [4rpy_T] [4rpy_D] [4rpy_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4RPY: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4RPY
  • Community annotation for 4RPY at PDBWiki (http://pdbwiki.org)

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