3KHR Dpo4 post-extension ternary complex with the correct C opposite the 2-aminofluorene-guanine [AF]G lesion date
authors Rechkoblit, O., Malinina, L., Patel, D.J.
compound source
R_Free 0.24650
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.01
ligand AF, CA, DDG, TTP enzyme
A, B

Primary referenceMechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4., Rechkoblit O, Kolbanovskiy A, Malinina L, Geacintov NE, Broyde S, Patel DJ, Nat Struct Mol Biol. 2010 Mar;17(3):379-88. Epub 2010 Feb 14. PMID:20154704
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (153 Kb) [Save to disk]
  • Biological Unit Coordinates (3khr.pdb1.gz) 72 Kb
  • Biological Unit Coordinates (3khr.pdb2.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 3KHR
  • CSU: Contacts of Structural Units for 3KHR
  • Structure Factors (466 Kb)
  • Retrieve 3KHR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KHR from S2C, [Save to disk]
  • Re-refined 3khr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KHR 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 3KHR
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3KHR, from MSDmotif at EBI
  • Fold representative 3khr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3khr_J] [3khr] [3khr_A] [3khr_D] [3khr_H] [3khr_E] [3khr_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3KHR
  • Community annotation for 3KHR at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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