PDBe 4boz

X-ray diffraction
3.03Å resolution

Structure of OTUD2 OTU domain in complex with K11-linked di ubiquitin

Released:

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).

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin thioesterase OTU1 Chains: A, D
Molecule details ›
Chains: A, D
Length: 183 amino acids
Theoretical weight: 20.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5VVQ6 (Residues: 132-314; Coverage: 53%)
Gene names: DUBA8, HIN7, OTUD2, PRO0907, YOD1
Sequence domains: OTU-like cysteine protease
Structure domains: Cathepsin B; Chain A
Ubiquitin Chains: B, C, E
Molecule details ›
Chains: B, C, E
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: C2
Unit cell:
a: 174.79Å b: 44.22Å c: 84.95Å
α: 90° β: 91.41° γ: 90°
R-values:
R R work R free
0.196 0.193 0.254
Expression system: Escherichia coli BL21(DE3)