4F5R Open and closed ternary complex of R283K DNA polymerase beta with a dCTP analog in the same asymmetric unit date
authors Freudenthal, B.D., Beard, W.A., Wilson, S.H.
compound source
symmetry
R_factor
R_Free 0.2776
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.20
ligand 6CF, MN, NA enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


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] (144 Kb) [Save to disk]
  • Biological Unit Coordinates (4f5r.pdb1.gz) 71 Kb
  • Biological Unit Coordinates (4f5r.pdb2.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 4F5R
  • CSU: Contacts of Structural Units for 4F5R
  • Structure Factors (782 Kb)
  • Retrieve 4F5R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4F5R from S2C, [Save to disk]
  • Re-refined 4f5r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4F5R 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 4F5R
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4F5R, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4f5r] [4f5r_C] [4f5r_P] [4f5r_D] [4f5r_G] [4f5r_A] [4f5r_B] [4f5r_T] [4f5r_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4F5R: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4F5R
  • Community annotation for 4F5R at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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