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 Diffraction	resolution	2.35 Å
ligand	MG, NO3	enzyme	Hydrolase E.C.3.4.19.12 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	OTU 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] (87 Kb) [Save to disk] Biological Unit Coordinates (4bos.pdb1.gz) 81 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

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 4BOS, from MSDmotif at EBI

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

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