› 4g1c

X-ray diffraction
1.94Å resolution

Human SIRT5 bound to Succ-IDH2 and Carba-NAD

Released:
DOI: 10.2210/pdb4g1c/pdb
PDB entry 4g1c coloured by chain, front view.
PDB entry 4g1c coloured by chain, side view.
PDB entry 4g1c coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Synthesis of carba-NAD and the structures of its ternary complexes with SIRT3 and SIRT5.
Szczepankiewicz BG, Dai H, Koppetsch KJ, Qian D, Jiang F, Mao C, Perni RB
J Org Chem 77 7319-29 (2012)
PMID: 22849721

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-164483 (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: 267 amino acids
Theoretical weight: 29.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NXA8 (Residues: 36-302; Coverage: 86%)
Gene names: SIR2L5, SIRT5
Sequence domains: Sir2 family
Structure domains:
Succinylated IDH2 peptide Chains: D, E
Molecule details ›
Chains: D, E
Length: 7 amino acids
Theoretical weight: 615 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand CNA 1 x CNA
1 modified residue:
Ligand SLL 2 x SLL

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P212121
Unit cell:
a: 67.239Å b: 84.425Å c: 95.74Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.194 0.242
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

10 review citations

Metabolic mechanisms of epigenetic regulation.
Meier JL. (2013)
9 more

5 mentions without citation

NAD Analogs in Aid of Chemical Biology and Medicinal Chemistry.
Depaix et al. (2019)
4 more