› 3v6c

X-ray diffraction
1.7Å resolution

Crystal Structure of USP2 in complex with mutated ubiquitin

Released:
DOI: 10.2210/pdb3v6c/pdb
PDB entry 3v6c coloured by chain, front view.
PDB entry 3v6c coloured by chain, side view.
PDB entry 3v6c coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Neculai M, Ernst A, Sidhu S, Arrowsmith CH, Edwards AM, Bountra C, Weigelt J, 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:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131078 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin carboxyl-terminal hydrolase 2 Chain: A
Molecule details ›
Chain: A
Length: 367 amino acids
Theoretical weight: 42.17 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O75604 (Residues: 258-605; Coverage: 58%)
Gene names: UBP41, USP2
Sequence domains: Ubiquitin carboxyl-terminal hydrolase
Structure domains: Cysteine proteinases
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 91 amino acids
Theoretical weight: 10.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG48 (Residues: 606-682; 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:
Ligand CL 2 x CL
Ligand GOL 1 x GOL
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P212121
Unit cell:
a: 57.735Å b: 84.077Å c: 86.915Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.176 0.22
Expression system: Escherichia coli BL21(DE3)

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