› 3rig

X-ray diffraction
2Å resolution

Sirt5 is an NAD-dependent protein lysine demalonylase and desuccinylase

Released:
DOI: 10.2210/pdb3rig/pdb
PDB entry 3rig coloured by chain, front view.
PDB entry 3rig coloured by chain, side view.
PDB entry 3rig coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase.
Du J, Zhou Y, Su X, Yu JJ, Khan S, Jiang H, Kim J, Woo J, Kim JH, Choi BH, He B, Chen W, Zhang S, Cerione RA, Auwerx J, Hao Q, Lin H
Science 334 806-9 (2011)
PMID: 22076378

Function and Biology Details

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-159446 (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%)
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: 1.29 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 5-16; Coverage: 9%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand NHE 2 x NHE
1 modified residue:
Ligand TLY 2 x TLY

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P212121
Unit cell:
a: 52.538Å b: 67.876Å c: 156.749Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.219 0.256
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

332 review citations

Sirtuins as regulators of metabolism and healthspan.
Houtkooper et al. (2012)
331 more

7 mentions without citation

Modulation of epigenetic targets for anticancer therapy: clinicopathological relevance, structural data and drug discovery perspectives.
Andreoli et al. (2013)
6 more