PDBe 3n3k

X-ray diffraction
2.6Å resolution

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

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin carboxyl-terminal hydrolase 8 Chain: A
Molecule details ›
Chain: A
Length: 396 amino acids
Theoretical weight: 45.42 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P40818 (Residues: 734-1110; Coverage: 34%)
Gene names: KIAA0055, UBPY, USP8
Sequence domains: Ubiquitin carboxyl-terminal hydrolase
Structure domains: Cysteine proteinases
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 85 amino acids
Theoretical weight: 9.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 533-608; 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: CLSI BEAMLINE 08ID-1
Spacegroup: P61
Unit cell:
a: 69.983Å b: 69.983Å c: 181.549Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.181 0.178 0.242
Expression system: Escherichia coli