PDBe 1nbf

X-ray diffraction
2.3Å resolution

Crystal structure of a UBP-family deubiquitinating enzyme in isolation and 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).
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin Chains: C, D
Molecule details ›
Chains: C, D
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
Ubiquitin carboxyl-terminal hydrolase 7 Chains: A, B, E
Molecule details ›
Chains: A, B, E
Length: 353 amino acids
Theoretical weight: 41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q93009 (Residues: 208-560; Coverage: 32%)
Gene names: HAUSP, USP7
Sequence domains: Ubiquitin carboxyl-terminal hydrolase
Structure domains: ubp-family deubiquitinating enzyme superfamily

Ligands and Environments

No bound ligands

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 99.728Å b: 101.166Å c: 141.134Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.218 0.262
Expression system: Escherichia coli