› 3pfy

X-ray diffraction
1.7Å resolution

The catalytic domain of human OTUD5

Released:
DOI: 10.2210/pdb3pfy/pdb
PDB entry 3pfy coloured by chain, front view.
PDB entry 3pfy coloured by chain, side view.
PDB entry 3pfy coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Walker JR, Asinas AE, Crombet L, Dong A, Weigelt J, Bountra C, Arrowsmith CH, Edwards AM, 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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188512 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
OTU domain-containing protein 5 Chain: A
Molecule details ›
Chain: A
Length: 185 amino acids
Theoretical weight: 22.32 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96G74 (Residues: 172-344; Coverage: 29%)
  • Best match: Q96G74-4 (Residues: 1-122)
Gene name: OTUD5
Sequence domains: OTU-like cysteine protease
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand PEG 2 x PEG
Ligand PG4 1 x PG4
Ligand SO4 1 x SO4
Ligand UNX 1 x UNX
1 modified residue:
Ligand MSE 9 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P41212
Unit cell:
a: 80.605Å b: 80.605Å c: 52.263Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.178 0.208
Expression system: Escherichia coli BL21(DE3)

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