3KHG Transferase Dna date Oct 30, 2009
title Dpo4 Extension Ternary Complex With Misinserted A Opposite T Aminofluorene-Guanine [Af]G Lesion
authors O.Rechkoblit, L.Malinina, D.J.Patel
compound source
Molecule: Dna Polymerase Iv
Chain: A, B
Synonym: Pol Iv
Engineered: Yes
Organism_scientific: Sulfolobus Solfataricus P2
Organism_taxid: 273057
Strain: P2 Dsm 1617 Jcm 11322
Gene: Dbh, Dpo4, Sso2448
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)-Ril(Stratagene)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: 5'-D(Gptptpgpgpaptpgpgptpapgp(2da))-
Chain: D, H
Engineered: Yes
Other_details: Dna Primer Strand (Dideoxy-Terminated At The

Synthetic: Yes
Other_details: Dna Primer Strand (Dideoxy-Terminated At The

Molecule: 5'-D(Ccptpapapcpgpcptpapcpcpaptpcp Cpc)-3';
Chain: E, J
Engineered: Yes
Other_details: Dna [Af]G-Modified Template Strand

Synthetic: Yes
Other_details: Dna [Af]G-Modified Template Strand
symmetry Space Group: P 1 21 1
R_factor 0.205 R_Free 0.282
length a length b length c angle alpha angle beta angle gamma
52.811 110.948 100.772 90.00 101.38 90.00
method X-Ray Diffractionresolution 2.96 Å
ligand 2DA, AF, CA, DGT, EPE enzyme Transferase E.C. BRENDA
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] (141 Kb) [Save to disk]
  • Biological Unit Coordinates (3khg.pdb1.gz) 69 Kb
  • Biological Unit Coordinates (3khg.pdb2.gz) 64 Kb
  • LPC: Ligand-Protein Contacts for 3KHG
  • CSU: Contacts of Structural Units for 3KHG
  • Structure Factors (177 Kb)
  • Retrieve 3KHG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KHG from S2C, [Save to disk]
  • Re-refined 3khg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KHG 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 3KHG
  • 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 3KHG, from MSDmotif at EBI
  • Fold representative 3khg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3khg_B] [3khg] [3khg_H] [3khg_J] [3khg_E] [3khg_D] [3khg_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3KHG
  • Community annotation for 3KHG 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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