4BOP Hydrolase date May 22, 2013
title Structure Of Otud1 Otu Domain
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: Otu Domain-Containing Protein 1
Chain: A, B
Fragment: Residues 287-437
Synonym: Duba-7, Otud1
Ec: 3.4.19.12
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
symmetry Space Group: I 4
R_factor 0.1616 R_Free 0.2023
crystal
cell
length a length b length c angle alpha angle beta angle gamma
82.240 82.240 103.940 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand PO4 enzyme Hydrolase E.C.3.4.19.12 BRENDA
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] (105 Kb) [Save to disk]
  • Biological Unit Coordinates (4bop.pdb1.gz) 399 Kb
  • LPC: Ligand-Protein Contacts for 4BOP
  • CSU: Contacts of Structural Units for 4BOP
  • Structure Factors (803 Kb)
  • Retrieve 4BOP in mmCIF format [Save to disk]
  • Re-refined 4bop structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4BOP 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 4BOP
  • 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 4BOP, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4bop_B] [4bop_A] [4bop]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4BOP
  • Community annotation for 4BOP 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, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science