PDBe 4f56

X-ray diffraction
1.7Å resolution

The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero dimer (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: 273 amino acids
Theoretical weight: 29.67 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NXA8 (Residues: 34-302; Coverage: 87%)
  • Best match: Q9NXA8-4 (Residues: 1-194)
Gene names: SIR2L5, SIRT5
Sequence domains: Sir2 family
Structure domains:
Histone H3.1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 12 amino acids
Theoretical weight: 1.24 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 5-16; Coverage: 9%)
Gene names: H3FA, H3FB, H3FC, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P212121
Unit cell:
a: 52.403Å b: 66.755Å c: 156.861Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.169 0.233
Expression systems:
  • Escherichia coli
  • Not provided