› 6nr0

X-ray diffraction
2.45Å resolution

SIRT2(56-356) with covalent intermediate between mechanism-based inhibitor Glucose-TM-1beta and 1'-SH ADP-ribose

Released:
DOI: 10.2210/pdb6nr0/pdb
Model geometry
Data not analysed
Fit model/data
Data not analysed
PDB entry 6nr0 coloured by chain, front view.
PDB entry 6nr0 coloured by chain, side view.
PDB entry 6nr0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A Glycoconjugated SIRT2 Inhibitor with Aqueous Solubility Allows Structure-Based Design of SIRT2 Inhibitors.
Hong JY, Price IR, Bai JJ, Lin H
ACS Chem Biol 14 1802-1810 (2019)
PMID: 31373792

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

Assemblies composition:
homo dimer
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184915 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NAD-dependent protein deacetylase sirtuin-2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 319 amino acids
Theoretical weight: 36.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8IXJ6 (Residues: 38-356; Coverage: 82%)
Gene names: SIR2L, SIR2L2, SIRT2
Sequence domains: Sir2 family

Ligands and Environments

6 bound ligands:
Ligand ZN 2 x ZN
Ligand KXJ 2 x KXJ
Ligand KXG 2 x KXG
Ligand NA 4 x NA
Ligand SO4 2 x SO4
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ALS BEAMLINE 5.0.3
Unit cell:
a: 82.31Å b: 76.84Å c: 114.461Å
α: 90° β: 95.874° γ: 90°
R-values:
R R work R free
0.223 0.22 0.256
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Discovering Anti-Cancer Drugs via Computational Methods.
Cui et al. (2020)
2 more

3 mentions without citation

Simultaneous Inhibition of SIRT2 Deacetylase and Defatty-Acylase Activities via a PROTAC Strategy.
Hong et al. (2020)
2 more