4BOS Hydrolase date May 22, 2013
title Structure Of Otud2 Otu Domain In Complex With Ubiquitin K11- Peptide
authors T.E.T.Mevissen, M.K.Hospenthal, P.P.Geurink, P.R.Elliott, M.Akut N.Arnaudo, R.Ekkebus, Y.Kulathu, T.Wauer, F.El Oualid, S.M.V.Fre H.Ovaa, D.Komander
compound source
Molecule: Ubiquitin Thioesterase Otu1
Chain: A, B
Fragment: Otu Domain, Residues 147-314
Synonym: Duba-8, Hiv-1-Induced Protease 7, Hin-7, Hshin7, O -Containing Protein 2, Otud2;
Ec: 3.4.19.12
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Rosetta Placi
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Popink

Molecule: Polyubiquitin-C
Chain: C, E
Fragment: Residues 1-76
Synonym: Otud2
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Rosetta Placi
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Popink

Molecule: Otud2
Chain: F
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Rosetta Placi
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Popink
symmetry Space Group: P 6
R_factor 0.187 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
164.480 164.480 44.730 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.35 Å
ligand MG, NO3 enzyme Hydrolase E.C.3.4.19.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceOTU Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis., Mevissen TE, Hospenthal MK, Geurink PP, Elliott PR, Akutsu M, Arnaudo N, Ekkebus R, Kulathu Y, Wauer T, El Oualid F, Freund SM, Ovaa H, Komander D, Cell. 2013 Jul 3;154(1):169-84. doi: 10.1016/j.cell.2013.05.046. PMID:23827681
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (88 Kb) [Save to disk]
  • Biological Unit Coordinates (4bos.pdb1.gz) 82 Kb
  • LPC: Ligand-Protein Contacts for 4BOS
  • CSU: Contacts of Structural Units for 4BOS
  • Structure Factors (1130 Kb)
  • Retrieve 4BOS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4BOS from S2C, [Save to disk]
  • Re-refined 4bos structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4BOS 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 4BOS
  • 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
  • 3D motif for 4BOS, from MSDmotif at EBI
  • Fold representative 4bos from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4bos_F] [4bos_E] [4bos] [4bos_B] [4bos_A] [4bos_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4BOS: [UBQ ] by SMART
  • Other resources with information on 4BOS
  • Community annotation for 4BOS at PDBWiki (http://pdbwiki.org)

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