3W31 Immune System date Dec 07, 2012
title Structual Basis For The Recognition Of Ubc13 By The Shigella Effector Ospi
authors A.Nishide, M.Kim, K.Takagi, C.Sasakawa, T.Mizushima
compound source
Molecule: Orf169b
Chain: A
Engineered: Yes
Mutation: Yes
 Organism_scientific: Shigella Flexneri
Organism_taxid: 623
Gene: Orf169b, Cp0209
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ubiquitin-Conjugating Enzyme E2 N
Chain: B
Synonym: Bendless-Like Ubiquitin-Conjugating Enzyme, Ubc13, Ubiquitin Carrier Protein N, Ubiquitin-Protein Ligase N;
Ec: 6.3.2.19
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2n, Blu
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 3 2 1
R_factor 0.245 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
119.238 119.238 69.985 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.96 Å
ligand IOD enzyme Ligase E.C.6.3.2.19 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceStructural Basis for the Recognition of Ubc13 by the Shigella flexneri Effector OspI., Nishide A, Kim M, Takagi K, Himeno A, Sanada T, Sasakawa C, Mizushima T, J Mol Biol. 2013 Aug 9;425(15):2623-31. doi: 10.1016/j.jmb.2013.02.037. Epub 2013, Mar 27. PMID:23542009
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (59 Kb) [Save to disk]
  • Biological Unit Coordinates (3w31.pdb1.gz) 54 Kb
  • LPC: Ligand-Protein Contacts for 3W31
  • CSU: Contacts of Structural Units for 3W31
  • Structure Factors (175 Kb)
  • Retrieve 3W31 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3W31 from S2C, [Save to disk]
  • Re-refined 3w31 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3W31 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 3W31
  • 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 3W31, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3w31_A] [3w31] [3w31_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3W31: [UBCc ] by SMART
    • Other resources with information on 3W31
  • Community annotation for 3W31 at PDBWiki (http://pdbwiki.org)

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