PDBe 5af6

X-ray diffraction
3.4Å resolution

Structure of Lys33-linked diUb bound to Trabid NZF1

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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 76 amino acids
Theoretical weight: 8.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Ubiquitin thioesterase ZRANB1 Chains: F, G, H, I, J
Molecule details ›
Chains: F, G, H, I, J
Length: 35 amino acids
Theoretical weight: 4.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UGI0 (Residues: 1-33; Coverage: 5%)
Gene names: TRABID, ZRANB1
Sequence domains: Zn-finger in Ran binding protein and others

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: C2
Unit cell:
a: 98.384Å b: 126.512Å c: 78.092Å
α: 90° β: 103.38° γ: 90°
R-values:
R R work R free
0.182 0.18 0.222
Expression system: Escherichia coli BL21(DE3)