4O3S Transferase Dna date Dec 18, 2013
title Crystal Structure Of Human Polymerase Eta Extending An 8-Oxo Lesion: Post Insertion Of 8-Oxog-Dc Pair
authors A.Patra, M.Egli
compound source
Molecule: Dna Polymerase Eta
Chain: A
Synonym: Rad30 Homolog A, Xeroderma Pigmentosum Variant Typ
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polh, Rad30, Rad30a, Xpv
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Cpaptpgp(8og)Ptpgpapcpgpcpt
Chain: T
Engineered: Yes
Other_details: Nucleic Acids Template: Cat G(8og)T Gac Gct

Synthetic: Yes
Other_details: Chemically Synthesized

Molecule: Dna (5'-D(Apgpcpgptpcpapc)-3')
Chain: P
Engineered: Yes
Other_details: Nucleic Acids Primar: Agcgtcac

Synthetic: Yes
Other_details: Chemically Synthesized
symmetry Space Group: P 61
R_factor 0.172 R_Free 0.210
length a length b length c angle alpha angle beta angle gamma
98.312 98.312 81.596 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.72 Å
ligand 0KX, 8OG, GOL, MG enzyme Transferase E.C. BRENDA

Primary referenceKinetics, Structure, and Mechanism of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA Polymerase eta, Patra A, Nagy LD, Zhang Q, Su Y, Muller L, Guengerich FP, Egli M, J Biol Chem. 2014 Jun 13;289(24):16867-16882. Epub 2014 Apr 23. PMID:24759104
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (95 Kb) [Save to disk]
  • Biological Unit Coordinates (4o3s.pdb1.gz) 88 Kb
  • LPC: Ligand-Protein Contacts for 4O3S
  • CSU: Contacts of Structural Units for 4O3S
  • Structure Factors (2364 Kb)
  • Retrieve 4O3S in mmCIF format [Save to disk]
  • Re-refined 4o3s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4O3S 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 4O3S
  • 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 4O3S, from MSDmotif at EBI
  • Fold representative 4o3s from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4o3s_P] [4o3s] [4o3s_A] [4o3s_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4O3S
  • Community annotation for 4O3S at PDBWiki (http://pdbwiki.org)

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