4Q8E Transferase Dna date Apr 26, 2014
title Human Dna Polymerase Eta Inserting Dcmpnpp Opposite A Phenan 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(Cpaptpgpcptpcpapcpapcpt)-3'
Chain: T
Engineered: Yes

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

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

Synthetic: Yes
Other_details: Synthesized By Sigma-Aldrich
symmetry Space Group: P 61
R_factor 0.183 R_Free 0.225
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.766 98.766 82.197 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.55 Å
ligand 0KX, GOL, MG, P9G enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


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] (94 Kb) [Save to disk]
  • Biological Unit Coordinates (4q8e.pdb1.gz) 89 Kb
  • LPC: Ligand-Protein Contacts for 4Q8E
  • CSU: Contacts of Structural Units for 4Q8E
  • Structure Factors (1115 Kb)
  • Retrieve 4Q8E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4Q8E from S2C, [Save to disk]
  • Re-refined 4q8e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4Q8E 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 4Q8E
  • 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 4Q8E, from MSDmotif at EBI
  • Fold representative 4q8e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4q8e] [4q8e_A] [4q8e_P] [4q8e_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4Q8E
  • Community annotation for 4Q8E at PDBWiki (http://pdbwiki.org)

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