› 5khy

X-ray diffraction
3.5Å resolution

Crystal structure of oxime-linked K6 diubiquitin

Released:
DOI: 10.2210/pdb5khy/pdb
PDB entry 5khy coloured by chain, front view.
PDB entry 5khy coloured by chain, side view.
PDB entry 5khy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Genetically Directed Production of Recombinant, Isosteric and Nonhydrolysable Ubiquitin Conjugates.
Stanley M, Virdee S
Chembiochem 17 1472-80 (2016)
PMID: 27197715

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143232 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin Chain: A
Molecule details ›
Chain: A
Length: 73 amino acids
Theoretical weight: 8.31 KDa
Source organism: Homo sapiens
Expression system: Bacteria
UniProt:
  • Canonical: P0CG47 (Residues: 153-225; Coverage: 32%)
Gene name: UBB
Sequence domains: Ubiquitin family
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 75 amino acids
Theoretical weight: 8.52 KDa
Source organism: Homo sapiens
Expression system: Bacteria
UniProt:
  • Canonical: P0CG47 (Residues: 153-227; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

2 bound ligands:
Ligand ZN 10 x ZN
Ligand ETA 1 x ETA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P4332
Unit cell:
a: 103.975Å b: 103.975Å c: 103.975Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.295 0.282 0.331
Expression system: Bacteria

Quick links

Citations

7 review citations

Oximes and Hydrazones in Bioconjugation: Mechanism and Catalysis.
Kölmel et al. (2017)
6 more

1 mention without citation

Genetically Directed Production of Recombinant, Isosteric and Nonhydrolysable Ubiquitin Conjugates.
Stanley et al. (2016)