› 4bn5

X-ray diffraction
3.25Å resolution

Structure of human SIRT3 in complex with SRT1720 inhibitor

Released:
DOI: 10.2210/pdb4bn5/pdb
PDB entry 4bn5 coloured by chain, front view.
PDB entry 4bn5 coloured by chain, side view.
PDB entry 4bn5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structures of human sirtuin 3 complexes with ADP-ribose and with carba-NAD+ and SRT1720: binding details and inhibition mechanism.
Nguyen GT, Schaefer S, Gertz M, Weyand M, Steegborn C
Acta Crystallogr D Biol Crystallogr 69 1423-32 (2013)
PMID: 23897466

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, G, H, I, J, K, L
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L
Length: 281 amino acids
Theoretical weight: 31.25 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9NTG7 (Residues: 119-399; Coverage: 70%)
Gene names: SIR2L3, SIRT3
Sequence domains: Sir2 family
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand CNA 12 x CNA
Ligand SR7 12 x SR7
Ligand ZN 12 x ZN
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: C2
Unit cell:
a: 227.82Å b: 246.06Å c: 127.34Å
α: 90° β: 123.88° γ: 90°
R-values:
R R work R free
0.211 0.208 0.265
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

15 review citations

The Role of Sirtuins in Antioxidant and Redox Signaling.
Singh et al. (2018)
14 more

5 mentions without citation

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