› 5l6h

X-ray diffraction
2.3Å resolution

Uba1 in complex with Ub-ABPA3 covalent adduct

Released:
DOI: 10.2210/pdb5l6h/pdb
PDB entry 5l6h coloured by chain, front view.
PDB entry 5l6h coloured by chain, side view.
PDB entry 5l6h coloured by chain, top view.
Source organisms:
Primary publication:
Dissecting the Specificity of Adenosyl Sulfamate Inhibitors Targeting the Ubiquitin-Activating Enzyme.
Misra M, Kuhn M, Löbel M, An H, Statsyuk AV, Sotriffer C, Schindelin H
Structure 25 1120-1129.e3 (2017)
PMID: 28578874

Function and Biology Details

Reaction catalysed: 
ATP + ubiquitin + [E1 ubiquitin-activating enzyme]-L-cysteine = AMP + diphosphate + S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138763 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin-activating enzyme E1 1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 1024 amino acids
Theoretical weight: 114.41 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P22515 (Residues: 1-1024; Coverage: 100%)
Gene names: UBA1, YKL210W
Sequence domains:
Structure domains:
Ubiquitin Chains: B, D, E
Molecule details ›
Chains: B, D, E
Length: 76 amino acids
Theoretical weight: 8.57 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P05759 (Residues: 1-76; Coverage: 50%)
Gene names: L9470.14, RPS31, RPS37, UBI3, YLR167W
Sequence domains: Ubiquitin family

Ligands and Environments

6 bound ligands:
Ligand SO4 2 x SO4
Ligand CL 8 x CL
Ligand GOL 11 x GOL
Ligand 6O2 2 x 6O2
Ligand MG 1 x MG
Ligand ACT 1 x ACT
1 modified residue:
Ligand CSO 2 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-3
Unit cell:
a: 72.048Å b: 194.098Å c: 230.172Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.175 0.172 0.218
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Targeting adenylate-forming enzymes with designed sulfonyladenosine inhibitors.
Lux et al. (2019)
4 more

1 mention without citation

Crystal structure of a human ubiquitin E1-ubiquitin complex reveals conserved functional elements essential for activity.
Lv et al. (2018)