› 6eo0

X-ray diffraction
2.4Å resolution

Zebrafish Sirt5 in complex with stalled peptidylimidate and bicyclic intermediate of inhibitory compound 29

Released:
DOI: 10.2210/pdb6eo0/pdb
PDB entry 6eo0 coloured by chain, front view.
PDB entry 6eo0 coloured by chain, side view.
PDB entry 6eo0 coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Mechanism-Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure-Activity Relationship, Biostructural, and Kinetic Insight.
Rajabi N, Auth M, Troelsen KR, Pannek M, Bhatt DP, Fontenas M, Hirschey MD, Steegborn C, Madsen AS, Olsen CA
Angew Chem Int Ed Engl 56 14836-14841 (2017)
PMID: 29044784

Function and Biology Details

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-179516 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NAD-dependent protein deacylase sirtuin-5, mitochondrial Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 277 amino acids
Theoretical weight: 30.68 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6DHI5 (Residues: 28-298; Coverage: 89%)
Gene names: si:ch211-121a2.1, sirt5
Sequence domains: Sir2 family
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand ZN 4 x ZN
Ligand EDO 4 x EDO
Ligand BV8 1 x BV8
Ligand BVT 4 x BVT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 64.93Å b: 113.59Å c: 72.31Å
α: 90° β: 103.24° γ: 90°
R-values:
R R work R free
0.255 0.253 0.305
Expression system: Escherichia coli

Quick links

Citations

8 review citations

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

2 mentions without citation

Mechanism-Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure-Activity Relationship, Biostructural, and Kinetic Insight.
Rajabi et al. (2017)
1 more