› 5d7n

X-ray diffraction
1.83Å resolution

Crystal structure of human Sirt3 at an improved resolution

Released:
DOI: 10.2210/pdb5d7n/pdb
PDB entry 5d7n coloured by chain, front view.
PDB entry 5d7n coloured by chain, side view.
PDB entry 5d7n coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking.
Rumpf T, Gerhardt S, Einsle O, Jung M
Acta Crystallogr F Struct Biol Commun 71 1498-510 (2015)
PMID: 26625292

Function and Biology Details

Reaction catalysed: 
(1a) [protein]-N(6)-acetyl-L-lysine + NAD(+) = [protein]-N(6)-(1,1-(5-adenosylyl-alpha-D-ribose-1,2-di-O-yl)ethyl)-L-lysine + nicotinamide
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192599 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NAD-dependent protein deacetylase sirtuin-3, mitochondrial Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 281 amino acids
Theoretical weight: 31.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NTG7 (Residues: 118-395; Coverage: 70%)
Gene names: SIR2L3, SIRT3
Sequence domains: Sir2 family
Structure domains:

Ligands and Environments

7 bound ligands:
Ligand ZN 6 x ZN
Ligand PEG 6 x PEG
Ligand MG 1 x MG
Ligand 1PE 1 x 1PE
Ligand GOL 1 x GOL
Ligand PGE 1 x PGE
Ligand PG4 1 x PG4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 84.99Å b: 143.85Å c: 89.46Å
α: 90° β: 116.33° γ: 90°
R-values:
R R work R free
0.176 0.175 0.203
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics.
Ali et al. (2018)
7 more

5 mentions without citation

Virtual Screening in the Identification of Sirtuins' Activity Modulators.
Abbotto et al. (2022)
4 more