3TMO	Hydrolase	date	Aug 31, 2011
title	The Catalytic Domain Of Human Deubiquitinase Duba
authors	J.Yin, I.Bosanac, X.Ma, S.Hymowitz, M.Starovasnik, A.Cochran
compound		source
Molecule: Otu Domain-Containing Protein 5 Chain: A Fragment: Catalytic Or Otu Domain (Residues 172-351) Synonym: Deubiquitinating Enzyme A, Duba Ec: 3.4.19.12 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Duba, Otud5 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21-Codonplus (De3)-Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28b
symmetry	Space Group: P 64	R_factor 0.243 R_Free 0.276
crystal cell	length a length b length c angle alpha angle beta angle gamma 66.658 66.658 82.218 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	MSE	enzyme	Hydrolase E.C.3.4.19.12 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Phosphorylation-dependent activity of the deubiquitinase DUBA., Huang OW, Ma X, Yin J, Flinders J, Maurer T, Kayagaki N, Phung Q, Bosanac I, Arnott D, Dixit VM, Hymowitz SG, Starovasnik MA, Cochran AG, Nat Struct Mol Biol. 2012 Jan 15;19(2):171-5. doi: 10.1038/nsmb.2206. PMID:22245969

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (31 Kb) [Save to disk] Biological Unit Coordinates (3tmo.pdb1.gz) 26 Kb Biological Unit Coordinates (3tmo.pdb2.gz) 50 Kb LPC: Ligand-Protein Contacts for 3TMO CSU: Contacts of Structural Units for 3TMO Structure Factors (438 Kb) Retrieve 3TMO in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3TMO from S2C, [Save to disk] Re-refined 3tmo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3TMO 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 3TMO

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 3TMO, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3tmo] [3tmo_A] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 3TMO

Community annotation for 3TMO at PDBWiki (http://pdbwiki.org)

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