X-ray diffraction
3.03Å resolution

Crystal structure of TRABID NZF1 in complex with K29 linked di-Ubiquitin


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: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
  • Canonical: P62987 (Residues: 1-76; Coverage: 59%)
Gene names: UBA52, UBCEP2
Sequence domains: Ubiquitin family
Ubiquitin thioesterase ZRANB1 Chains: F, G, H, I, J
Molecule details ›
Chains: F, G, H, I, J
Length: 36 amino acids
Theoretical weight: 4.1 KDa
Source organism: Bos taurus
  • Canonical: A6QP16 (Residues: 2-33; Coverage: 5%)
Gene name: 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 I04
Spacegroup: C2
Unit cell:
a: 99.222Å b: 123.971Å c: 78.312Å
α: 90° β: 103.68° γ: 90°
R R work R free
0.225 0.222 0.27
Expression system: Escherichia coli BL21(DE3)