› 5gxo

X-ray diffraction
2.3Å resolution

Discovery of a compound that activates SIRT3 to deacetylate Manganese Superoxide Dismutase

Released:
DOI: 10.2210/pdb5gxo/pdb
PDB entry 5gxo coloured by chain, front view.
PDB entry 5gxo coloured by chain, side view.
PDB entry 5gxo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A small molecule activator of SIRT3 promotes deacetylation and activation of manganese superoxide dismutase.
Lu J, Zhang H, Chen X, Zou Y, Li J, Wang L, Wu M, Zang J, Yu Y, Zhuang W, Xia Q, Wang J
Free Radic Biol Med 112 287-297 (2017)
PMID: 28711502

Function and Biology Details

Reaction catalysed: 
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-137484 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Superoxide dismutase [Mn], mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 198 amino acids
Theoretical weight: 22.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P04179 (Residues: 25-222; Coverage: 89%)
Gene name: SOD2
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand MN 2 x MN
1 modified residue:
Ligand ALY 2 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P6122
Unit cell:
a: 80.12Å b: 80.12Å c: 242.87Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.215 0.213 0.25
Expression system: Escherichia coli K-12

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Citations

11 review citations

NAD+ metabolism: pathophysiologic mechanisms and therapeutic potential.
Xie et al. (2020)
10 more