› 5h4d

X-ray diffraction
3.21Å resolution

Crystal structure of hSIRT3 in complex with a specific agonist Amiodarone hydrochloride

Released:
DOI: 10.2210/pdb5h4d/pdb
PDB entry 5h4d coloured by chain, front view.
PDB entry 5h4d coloured by chain, side view.
PDB entry 5h4d coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Zhang S, Fu L, Liu J, Liu B

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-165718 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
NAD-dependent protein deacetylase sirtuin-3, mitochondrial Chains: A, H
Molecule details ›
Chains: A, H
Length: 271 amino acids
Theoretical weight: 30.2 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NTG7 (Residues: 121-391; Coverage: 68%)
Gene names: SIR2L3, SIRT3
Sequence domains: Sir2 family
Structure domains:
ARG-HIS-LYS Chains: C, D
Molecule details ›
Chains: C, D
Length: 4 amino acids
Theoretical weight: 613 Da
Source organism: Homo sapiens
Expression system: Escherichia coli

Ligands and Environments

6 bound ligands:
Ligand ZN 2 x ZN
Ligand MG 2 x MG
Ligand BBI 2 x BBI
Ligand NAD 2 x NAD
Ligand MCM 2 x MCM
Ligand PEG 2 x PEG
1 modified residue:
Ligand ALY 2 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: R3
Unit cell:
a: 114.56Å b: 114.56Å c: 123.404Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.22 0.213 0.372
Expression system: Escherichia coli

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