PDBe 2ibi

X-ray diffraction
2.2Å resolution

Covalent Ubiquitin-USP2 Complex

Released:
Source organism: Homo sapiens
Entry authors: Walker JR, Avvakumov GV, Bernstein G, Xue S, Finerty Jr PJ, MacKenzie F, Weigelt J, Sundstrom M, 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).
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 2 Chain: A
Molecule details ›
Chain: A
Length: 374 amino acids
Theoretical weight: 42.71 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O75604 (Residues: 251-605; Coverage: 59%)
Gene names: UBP41, USP2
Sequence domains: Ubiquitin carboxyl-terminal hydrolase
Structure domains: Cysteine proteinases
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 75 amino acids
Theoretical weight: 8.52 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
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

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: C2
Unit cell:
a: 102.839Å b: 54.4Å c: 75.021Å
α: 90° β: 107.66° γ: 90°
R-values:
R R work R free
0.194 0.19 0.259
Expression system: Escherichia coli BL21(DE3)