PDBe 3tmp

X-ray diffraction
1.91Å resolution

The catalytic domain of human deubiquitinase DUBA in complex with ubiquitin aldehyde

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).
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
OTU domain-containing protein 5 Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 184 amino acids
Theoretical weight: 21.26 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
Ubiquitin Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 76 amino acids
Theoretical weight: 8.56 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
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

No bound ligands

2 modified residues:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P1
Unit cell:
a: 59.532Å b: 65.296Å c: 65.843Å
α: 90.26° β: 93.53° γ: 99.28°
R-values:
R R work R free
0.192 0.19 0.227
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli