PDBe 3ihp

X-ray diffraction
2.8Å resolution

Covalent Ubiquitin-Usp5 Complex

Released:
Source organism: Homo sapiens
Entry authors: Walker JR, Avvakumov GV, Xue S, Butler-Cole C, Weigelt J, Bountra C, Arrowsmith CH, Edwards AM, Bochkarev A, Dhe-Paganon S, Structural Genomics Consortium (SGC)

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:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin carboxyl-terminal hydrolase 5 Chains: A, B
Molecule details ›
Chains: A, B
Length: 854 amino acids
Theoretical weight: 95.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P45974 (Residues: 1-858; Coverage: 97%)
  • Best match: P45974-2 (Residues: 1-835)
Gene names: ISOT, USP5
Sequence domains:
Structure domains:
Ubiquitin Chains: C, D
Molecule details ›
Chains: C, D
Length: 75 amino acids
Theoretical weight: 8.52 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-683; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P212121
Unit cell:
a: 68.295Å b: 188.845Å c: 207.86Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.224 0.276
Expression system: Escherichia coli