› 5qit

X-ray diffraction
1.46Å resolution

Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0102821

Released:
DOI: 10.2210/pdb5qit/pdb
PDB entry 5qit coloured by chain, front view.
PDB entry 5qit coloured by chain, side view.
PDB entry 5qit coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Sethi R, Douangamath A, Resnick E, Bradley AR, Collins P, Brandao-Neto J, Talon R, Krojer T, Bountra C, Arrowsmith CH, Edwards A, London N, von Delft F

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:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188434 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin thioesterase OTUB2 Chain: A
Molecule details ›
Chain: A
Length: 225 amino acids
Theoretical weight: 26.36 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96DC9 (Residues: 6-230; Coverage: 96%)
Gene names: C14orf137, OTB2, OTU2, OTUB2
Sequence domains: Peptidase C65 Otubain

Ligands and Environments

3 bound ligands:
Ligand J5J 1 x J5J
Ligand EDO 3 x EDO
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P21
Unit cell:
a: 47.289Å b: 58.436Å c: 49.713Å
α: 90° β: 115.87° γ: 90°
R-values:
R R work R free
0.144 0.142 0.195
Expression system: Escherichia coli

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