PDBe 4bos

X-ray diffraction
2.35Å resolution

Structure of OTUD2 OTU domain in complex with Ubiquitin K11-linked peptide

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

Assembly composition:
hetero pentamer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin thioesterase OTU1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 169 amino acids
Theoretical weight: 19.09 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5VVQ6 (Residues: 147-314; Coverage: 48%)
Gene names: DUBA8, HIN7, OTUD2, PRO0907, YOD1
Sequence domains: OTU-like cysteine protease
Structure domains: Cathepsin B; Chain A
Ubiquitin Chains: C, E
Molecule details ›
Chains: 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
Ubiquitin Chain: F
Molecule details ›
Chain: F
Length: 14 amino acids
Theoretical weight: 1.55 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG48 (Residues: 612-625; Coverage: 2%)
Gene name: UBC

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P6
Unit cell:
a: 164.48Å b: 164.48Å c: 44.73Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.189 0.187 0.238
Expression system: Escherichia coli BL21(DE3)