PDBe 5cvn

X-ray diffraction
3.36Å resolution

WDR48 (2-580):USP46~ubiquitin ternary complex

Released:

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 trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
WD repeat-containing protein 48 Chain: A
Molecule details ›
Chain: A
Length: 598 amino acids
Theoretical weight: 67.15 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8TAF3 (Residues: 2-580; Coverage: 86%)
  • Best match: Q8TAF3-2 (Residues: 1-22)
Gene names: KIAA1449, UAF1, WDR48
Sequence domains: WD domain, G-beta repeat
Ubiquitin carboxyl-terminal hydrolase 46 Chain: B
Molecule details ›
Chain: B
Length: 358 amino acids
Theoretical weight: 41.96 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P62068 (Residues: 25-366; Coverage: 93%)
  • Best match: P62068-2 (Residues: 1-217)
Gene name: USP46
Sequence domains: Ubiquitin carboxyl-terminal hydrolase
Structure domains: Cysteine proteinases
Ubiquitin Chain: D
Molecule details ›
Chain: D
Length: 96 amino acids
Theoretical weight: 10.75 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: I222
Unit cell:
a: 103.437Å b: 154.189Å c: 182.854Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.175 0.222
Expression system: Trichoplusia ni