› 6flg

X-ray diffraction
2.5Å resolution

Crystal structure of zebrafish Sirtuin 5 in complex with 3(S)-(naphthylthio)succinyl-CPS1 peptide

Released:
DOI: 10.2210/pdb6flg/pdb
PDB entry 6flg coloured by chain, front view.
PDB entry 6flg coloured by chain, side view.
PDB entry 6flg coloured by chain, top view.
Source organisms:
Primary publication:
Potent and Selective Inhibitors of Human Sirtuin 5.
Kalbas D, Liebscher S, Nowak T, Meleshin M, Pannek M, Popp C, Alhalabi Z, Bordusa F, Sippl W, Steegborn C, Schutkowski M
J Med Chem 61 2460-2471 (2018)
PMID: 29494161

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179516 (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: 284 amino acids
Theoretical weight: 31.5 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6DHI5 (Residues: 28-305; Coverage: 91%)
Gene names: si:ch211-121a2.1, sirt5
Sequence domains: Sir2 family
Structure domains:
3(S)-(naphthylthio)succinyl-CPS1 peptide Chain: C
Molecule details ›
Chain: C
Length: 8 amino acids
Theoretical weight: 1.21 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand ZN 2 x ZN
Ligand EDO 3 x EDO
Ligand DMS 1 x DMS
Ligand EPE 1 x EPE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P6522
Unit cell:
a: 87Å b: 87Å c: 316.88Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.245 0.242 0.311
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Functions of the sirtuin deacylase SIRT5 in normal physiology and pathobiology.
Kumar et al. (2018)
5 more