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;
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
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. BRENDA


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] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (3w31.pdb1.gz) 55 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
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  • Visual 3D analysis of 3W31
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  • 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 3W31, from MSDmotif at EBI
  • Fold representative 3w31 from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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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