4Q8F Transferase Dna date Apr 26, 2014
title Human Dna Polymerase Eta Extending Primer Immediately After Phenanthriplatin Adducted G
authors M.T.Gregory, W.Yang
compound source
Molecule: Dna Polymerase Eta
Chain: A
Synonym: Rad30 Homolog A, Xeroderma Pigmentosum Variant Typ
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polh, Polh Rad30 Rad30a Xpv, Rad30, Rad30a, Xpv
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28

Molecule: 5'-D(Cpaptpcpgptpcpapcpapcpt)-3'
Chain: T
Engineered: Yes

Synthetic: Yes
Other_details: Synthesized By Sigma-Aldrich And Adducted Wi Phenanthriplatin;

Molecule: 5'-D(Apgptpgptpgpapc)-3'
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: Synthesized By Sigma-Aldrich
symmetry Space Group: P 61
R_factor 0.196 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.692 98.692 81.812 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.80 Å
ligand GOL, MG, P9G, XG4 enzyme Transferase E.C.2.7.7.7 BRENDA
Primary referenceStructural and mechanistic studies of polymerase eta bypass of phenanthriplatin DNA damage., Gregory MT, Park GY, Johnstone TC, Lee YS, Yang W, Lippard SJ, Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):9133-8. doi:, 10.1073/pnas.1405739111. Epub 2014 Jun 9. PMID:24927576
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (4q8f.pdb1.gz) 80 Kb
  • LPC: Ligand-Protein Contacts for 4Q8F
  • CSU: Contacts of Structural Units for 4Q8F
  • Structure Factors (384 Kb)
  • Retrieve 4Q8F in mmCIF format [Save to disk]
  • Re-refined 4q8f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4Q8F 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 4Q8F
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4Q8F, from MSDmotif at EBI
  • Fold representative 4q8f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4q8f_P] [4q8f_T] [4q8f_A] [4q8f]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4Q8F
  • Community annotation for 4Q8F at PDBWiki (http://pdbwiki.org)

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