› 3tmo

X-ray diffraction
2.2Å resolution

The catalytic domain of human deubiquitinase DUBA

Released:
DOI: 10.2210/pdb3tmo/pdb
PDB entry 3tmo coloured by chain, front view.
PDB entry 3tmo coloured by chain, side view.
PDB entry 3tmo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
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 19 171-5 (2012)
PMID: 22245969

Function and Biology Details

Reaction catalysed: 
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-188512 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
OTU domain-containing protein 5 Chain: A
Molecule details ›
Chain: A
Length: 184 amino acids
Theoretical weight: 21.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96G74 (Residues: 172-351; Coverage: 32%)
Gene name: OTUD5
Sequence domains: OTU-like cysteine protease
Structure domains:

Ligands and Environments

No bound ligands
1 modified residue:
Ligand MSE 9 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P64
Unit cell:
a: 66.658Å b: 66.658Å c: 82.218Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.245 0.243 0.276
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

19 review citations

Deubiquitylases from genes to organism.
Clague et al. (2013)
18 more