› 4fz3

X-ray diffraction
2.1Å resolution

Crystal structure of SIRT3 in complex with acetyl p53 peptide coupled with 4-amino-7-methylcoumarin

Released:
DOI: 10.2210/pdb4fz3/pdb
PDB entry 4fz3 coloured by chain, front view.
PDB entry 4fz3 coloured by chain, side view.
PDB entry 4fz3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery and mechanism study of SIRT1 activators that promote the deacetylation of fluorophore-labeled substrate.
Wu J, Zhang D, Chen L, Li J, Wang J, Ning C, Yu N, Zhao F, Chen D, Chen X, Chen K, Jiang H, Liu H, Liu D
J Med Chem 56 761-80 (2013)
PMID: 23316803

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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138127 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
NAD-dependent protein deacetylase sirtuin-3, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 283 amino acids
Theoretical weight: 31.4 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NTG7 (Residues: 118-399; Coverage: 71%)
Gene names: SIR2L3, SIRT3
Sequence domains: Sir2 family
Structure domains:
Cellular tumor antigen p53 Chain: B
Molecule details ›
Chain: B
Length: 6 amino acids
Theoretical weight: 796 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P04637 (Residues: 379-382; Coverage: 1%)
Gene names: P53, TP53

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
1 modified residue:
Ligand ALY 1 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: R32
Unit cell:
a: 114.809Å b: 114.809Å c: 123.202Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.211 0.208 0.282
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Small-molecule allosteric activators of sirtuins.
Sinclair et al. (2014)
3 more

1 mention without citation

Comparative modeling and benchmarking data sets for human histone deacetylases and sirtuin families.
Xia et al. (2015)