4F5P Open ternary mismatch complex of R283K DNA polymerase beta with a dATP analog date
authors Freudenthal, B.D., Beard, W.A., Wilson, S.H.
compound source
symmetry
R_factor
R_Free 0.2452
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.85
ligand F2A, MG, NA BindingDB enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructures of dNTP Intermediate States during DNA Polymerase Active Site Assembly., Freudenthal BD, Beard WA, Wilson SH, Structure. 2012 Nov 7;20(11):1829-37. doi: 10.1016/j.str.2012.08.008. Epub 2012, Sep 6. PMID:22959623
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (4f5p.pdb1.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 4F5P
  • CSU: Contacts of Structural Units for 4F5P
  • Structure Factors (360 Kb)
  • Retrieve 4F5P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4F5P from S2C, [Save to disk]
  • Re-refined 4f5p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4F5P 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 4F5P
  • 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 4F5P, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4f5p_A] [4f5p_D] [4f5p_P] [4f5p] [4f5p_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4F5P: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4F5P
  • Community annotation for 4F5P at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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