› 4rxx

X-ray diffraction
2.06Å resolution

Crystal Structure of the N-terminal Domain of Human Ubiquitin Specific Protease 38

Released:
DOI: 10.2210/pdb4rxx/pdb
PDB entry 4rxx coloured by chain, front view.
PDB entry 4rxx coloured by chain, side view.
PDB entry 4rxx coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Dong A, Shen L, Hu J, 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

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185457 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin carboxyl-terminal hydrolase 38 Chain: A
Molecule details ›
Chain: A
Length: 430 amino acids
Theoretical weight: 49.56 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8NB14 (Residues: 1-424; Coverage: 41%)
Gene names: KIAA1891, USP38
Sequence domains: Ubiquitin carboxyl-terminal hydrolase 38-like, N-terminal domain

Ligands and Environments

3 bound ligands:
Ligand CL 1 x CL
Ligand EDO 1 x EDO
Ligand UNX 5 x UNX
1 modified residue:
Ligand MSE 10 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 41.985Å b: 102.039Å c: 135.281Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.189 0.242
Expression system: Escherichia coli BL21(DE3)

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