› 5vbd

X-ray diffraction
1.5Å resolution

Crystal structure of a putative UBL domain of USP9X

Released:
DOI: 10.2210/pdb5vbd/pdb
PDB entry 5vbd coloured by chain, front view.
PDB entry 5vbd coloured by chain, side view.
PDB entry 5vbd coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Dong A, Chern Y, Hou F, Li Y, Tempel W, Bountra C, Arrowsmith CH, Edwards AM, Tong Y, 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 domain:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-187969 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin carboxyl-terminal hydrolase 9X Chain: A
Molecule details ›
Chain: A
Length: 109 amino acids
Theoretical weight: 12.44 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q93008 (Residues: 880-970; Coverage: 4%)
Gene names: DFFRX, FAM, USP9, USP9X

Ligands and Environments

1 bound ligand:
Ligand UNX 3 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: C2221
Unit cell:
a: 46.723Å b: 125.294Å c: 29.546Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.227 0.236
Expression system: Escherichia coli BL21(DE3)

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