5IIO Transferase Dna date Mar 01, 2016
title Crystal Structure Of The Dna Polymerase Lambda Binary Comple
authors M.J.Burak, K.E.Guja, M.Garcia-Diaz
compound source
Molecule: Dna (5'-D(Cpgpgpcp(8og)Pgptpapcptpg)-3
Chain: B, F, J, N
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Cpapgptpapc)-3')
Chain: C, G, K, O
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Pgpcpcpg)-3')
Chain: D, H, L, P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna Polymerase Lambda
Chain: A, E, I, M
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)
symmetry Space Group: P 21 21 2
R_factor 0.191 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
191.423 98.980 105.034 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.08 Å
ligand 8OG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, M, I, E


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] (272 Kb) [Save to disk]
  • Biological Unit Coordinates (5iio.pdb1.gz) 71 Kb
  • Biological Unit Coordinates (5iio.pdb2.gz) 67 Kb
  • Biological Unit Coordinates (5iio.pdb3.gz) 68 Kb
  • Biological Unit Coordinates (5iio.pdb4.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 5IIO
  • CSU: Contacts of Structural Units for 5IIO
  • Structure Factors (2435 Kb)
  • Retrieve 5IIO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5IIO from S2C, [Save to disk]
  • Re-refined 5iio structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5IIO 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 5IIO
  • 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 5iio from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5iio_F] [5iio_B] [5iio_L] [5iio] [5iio_H] [5iio_J] [5iio_K] [5iio_O] [5iio_C] [5iio_N] [5iio_E] [5iio_G] [5iio_I] [5iio_D] [5iio_P] [5iio_M] [5iio_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5IIO: [HhH1] [POLXc ] by SMART
  • Other resources with information on 5IIO
  • Community annotation for 5IIO at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science