2I9G Transferase Dna date Sep 05, 2006
title Dna Polymerase Beta With A Benzo[C]Phenanthrene Diol Epoxide Guanine Base
authors V.K.Batra, S.H.Wilson, W.A.Beard, L.C.Pedersen
compound source
Molecule: 5'-D(Pgptpcpgpg)-3'
Chain: D
Engineered: Yes
Synthetic: Yes

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

Synthetic: Yes

Molecule: 5'-D(Cpcpgpapcpgpgpcpgpcpaptpcpapg
Chain: T
Engineered: Yes

Synthetic: Yes

Molecule: Dna Polymerase Beta
Chain: A
Ec: 2.7.7.7
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.200 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.550 78.900 54.950 90.00 105.63 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand BPI, CL, DOC, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure of DNA polymerase beta with a benzo[c]phenanthrene diol epoxide-adducted template exhibits mutagenic features., Batra VK, Shock DD, Prasad R, Beard WA, Hou EW, Pedersen LC, Sayer JM, Yagi H, Kumar S, Jerina DM, Wilson SH, Proc Natl Acad Sci U S A. 2006 Nov 14;103(46):17231-6. Epub 2006 Nov 1. PMID:17079493
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (2i9g.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 2I9G
  • CSU: Contacts of Structural Units for 2I9G
  • Likely Quarternary Molecular Structure file(s) for 2I9G
  • Structure Factors (355 Kb)
  • Retrieve 2I9G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2I9G from S2C, [Save to disk]
  • Re-refined 2i9g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2I9G 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 2I9G
  • 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
  • 3D motif for 2I9G, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2i9g_A] [2i9g_P] [2i9g_D] [2i9g_T] [2i9g]
  • SWISS-PROT database: [P06746]
  • Domain organization of [DPOLB_HUMAN] by SWISSPFAM
  • Domains found in 2I9G: [HhH1] [POLXc ] by SMART
  • Other resources with information on 2I9G
  • Community annotation for 2I9G 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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