5IIJ Transferase Dna date Mar 01, 2016
title Crystal Structure Of The Pre-Catalytic Ternary Complex Of Dn Polymerase Lambda With A Templating 8-Oxo-Dg And An Incomin
authors M.J.Burak, K.E.Guja, M.Garcia-Diaz
compound source
Molecule: Dna Polymerase Lambda
Chain: A
Synonym: Pol Lambda,Dna Polymerase Beta-2,Pol Beta2,Dna Pol Kappa;
Ec: 2.7.7.7,4.2.99.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Poll
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Dna (5'-D(Pgpcpcpg)-3')
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Cpapgptpap(Doc))-3')
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Cpgpgpcp(8og)Pgptpapcptpg)-3
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.197 R_Free 0.224
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.749 62.850 140.076 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.72 Å
ligand 8OG, DCT, DOC, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceA fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG., Burak MJ, Guja KE, Hambardjieva E, Derkunt B, Garcia-Diaz M, EMBO J. 2016 Aug 1. pii: e201694332. PMID:27481934
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (5iij.pdb1.gz) 67 Kb
  • LPC: Ligand-Protein Contacts for 5IIJ
  • CSU: Contacts of Structural Units for 5IIJ
  • Structure Factors (1092 Kb)
  • Retrieve 5IIJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5IIJ from S2C, [Save to disk]
  • Re-refined 5iij structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5IIJ 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 5IIJ
  • 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
  • Fold representative 5iij from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5iij] [5iij_D] [5iij_T] [5iij_A] [5iij_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5IIJ: [HhH1] [POLXc ] by SMART
  • Other resources with information on 5IIJ
  • Community annotation for 5IIJ at PDBWiki (http://pdbwiki.org)

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