› 5f6x

X-ray diffraction
1.56Å resolution

Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole from cocktail screen)

Released:
DOI: 10.2210/pdb5f6x/pdb
PDB entry 5f6x coloured by chain, front view.
PDB entry 5f6x coloured by chain, side view.
PDB entry 5f6x coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9.
Hewitt WM, Lountos GT, Zlotkowski K, Dahlhauser SD, Saunders LB, Needle D, Tropea JE, Zhan C, Wei G, Ma B, Nussinov R, Waugh DS, Schneekloth JS
Angew Chem Int Ed Engl 55 5703-7 (2016)
PMID: 27038327

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159073 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
SUMO-conjugating enzyme UBC9 Chain: A
Molecule details ›
Chain: A
Length: 157 amino acids
Theoretical weight: 17.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P63279 (Residues: 2-158; Coverage: 99%)
Gene names: UBC9, UBCE9, UBE2I
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme

Ligands and Environments

1 bound ligand:
Ligand 5VM 1 x 5VM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 50.48Å b: 35.558Å c: 58.11Å
α: 90° β: 111.64° γ: 90°
R-values:
R R work R free
0.175 0.174 0.193
Expression system: Escherichia coli

Quick links

Citations

3 review citations

The Molecular Basis of Ubiquitin-Conjugating Enzymes (E2s) as a Potential Target for Cancer Therapy.
Du et al. (2021)
2 more

1 mention without citation

Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9.
Hewitt et al. (2016)