› 4rmj

X-ray diffraction
1.87Å resolution

Human Sirt2 in complex with ADP ribose and nicotinamide

Released:
DOI: 10.2210/pdb4rmj/pdb
PDB entry 4rmj coloured by chain, front view.
PDB entry 4rmj coloured by chain, side view.
PDB entry 4rmj coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Selective Sirt2 inhibition by ligand-induced rearrangement of the active site.
Rumpf T, Schiedel M, Karaman B, Roessler C, North BJ, Lehotzky A, Oláh J, Ladwein KI, Schmidtkunz K, Gajer M, Pannek M, Steegborn C, Sinclair DA, Gerhardt S, Ovádi J, Schutkowski M, Sippl W, Einsle O, Jung M
Nat Commun 6 6263 (2015)
PMID: 25672491

Function and Biology Details

Reaction catalysed: 
(1a) [protein]-N(6)-acetyl-L-lysine + NAD(+) = [protein]-N(6)-(1,1-(5-adenosylyl-alpha-D-ribose-1,2-di-O-yl)ethyl)-L-lysine + nicotinamide
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184916 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NAD-dependent protein deacetylase sirtuin-2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 304 amino acids
Theoretical weight: 34.42 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8IXJ6 (Residues: 56-356; Coverage: 77%)
Gene names: SIR2L, SIR2L2, SIRT2
Sequence domains: Sir2 family
Structure domains:

Ligands and Environments

7 bound ligands:
Ligand AR6 2 x AR6
Ligand NCA 1 x NCA
Ligand PEG 1 x PEG
Ligand EDO 3 x EDO
Ligand NA 1 x NA
Ligand ZN 2 x ZN
Ligand PGE 1 x PGE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 77.6Å b: 77.96Å c: 114.28Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.21 0.24
Expression system: Escherichia coli

Quick links

Citations

31 review citations

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

4 mentions without citation

Selective Sirt2 inhibition by ligand-induced rearrangement of the active site.
Rumpf et al. (2015)
3 more