4BOZ Hydrolase date May 22, 2013
title Structure Of Otud2 Otu Domain In Complex With K11-Linked Di
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, D
Fragment: Residues 132-314
Synonym: Otud2, Duba-8, Hiv-1-Induced Protease 7, Hin-7, Hs Otu Domain-Containing Protein 2;
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_vector: Popink

Molecule: Ubiquitin-C
Chain: B, C, E
Synonym: Ubiquitin
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_vector: Pet17b
symmetry Space Group: C 1 2 1
R_factor 0.1933 R_Free 0.2544
crystal
cell
length a length b length c angle alpha angle beta angle gamma
174.790 44.220 84.950 90.00 91.41 90.00
method X-Ray Diffractionresolution 3.03 Å
ligand GOL enzyme Hydrolase E.C.3.4.19.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D


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] (179 Kb) [Save to disk]
  • Biological Unit Coordinates (4boz.pdb1.gz) 74 Kb
  • Biological Unit Coordinates (4boz.pdb2.gz) 81 Kb
  • Biological Unit Coordinates (4boz.pdb3.gz) 23 Kb
  • LPC: Ligand-Protein Contacts for 4BOZ
  • CSU: Contacts of Structural Units for 4BOZ
  • Structure Factors (491 Kb)
  • Retrieve 4BOZ in mmCIF format [Save to disk]
  • Re-refined 4boz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4BOZ 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 4BOZ
  • 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 4BOZ, from MSDmotif at EBI
  • Fold representative 4boz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4boz_E] [4boz] [4boz_B] [4boz_D] [4boz_C] [4boz_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4BOZ: [UBQ ] by SMART
  • Other resources with information on 4BOZ
  • Community annotation for 4BOZ at PDBWiki (http://pdbwiki.org)

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