› 4hda

X-ray diffraction
2.6Å resolution

Crystal structure of human Sirt5 in complex with Fluor-de-Lys peptide and resveratrol

Released:
DOI: 10.2210/pdb4hda/pdb
PDB entry 4hda coloured by chain, front view.
PDB entry 4hda coloured by chain, side view.
PDB entry 4hda coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A molecular mechanism for direct sirtuin activation by resveratrol.
Gertz M, Nguyen GT, Fischer F, Suenkel B, Schlicker C, Fränzel B, Tomaschewski J, Aladini F, Becker C, Wolters D, Steegborn C
PLoS One 7 e49761 (2012)
PMID: 23185430

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-164542 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
NAD-dependent protein deacylase sirtuin-5, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 275 amino acids
Theoretical weight: 29.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9NXA8 (Residues: 34-302; Coverage: 87%)
Gene names: SIR2L5, SIRT5
Sequence domains: Sir2 family
Structure domains:
Fluor-de-Lys peptide Chain: F
Molecule details ›
Chain: F
Length: 4 amino acids
Theoretical weight: 770 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand STL 1 x STL
1 modified residue:
Ligand FDL 1 x FDL

Experiments and Validation Details

Entry percentile scores
X-ray source: OTHER
Spacegroup: P21
Unit cell:
a: 41.3Å b: 112.69Å c: 55.89Å
α: 90° β: 90.05° γ: 90°
R-values:
R R work R free
0.205 0.199 0.252
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

64 review citations

Epigenetics and aging.
Pal et al. (2016)
63 more

7 mentions without citation

Sirtuin activators and inhibitors: Promises, achievements, and challenges.
Dai et al. (2018)
6 more