› 5dhu

X-ray diffraction
2.33Å resolution

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a novel inhibitor

Released:
DOI: 10.2210/pdb5dhu/pdb
PDB entry 5dhu coloured by chain, front view.
PDB entry 5dhu coloured by chain, side view.
PDB entry 5dhu coloured by chain, top view.
Source organism: Listeria monocytogenes EGD-e
Primary publication:
8-Thioalkyl-adenosine derivatives inhibit Listeria monocytogenes NAD kinase through a novel binding mode.
Paoletti J, Assairi L, Gelin M, Huteau V, Nahori MA, Dussurget O, Labesse G, Pochet S
Eur J Med Chem 124 1041-1056 (2016)
PMID: 27783975

Function and Biology Details

Reaction catalysed: 
ATP + NAD(+) = ADP + NADP(+)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-570941 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NAD kinase 1 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 272 amino acids
Theoretical weight: 31.05 KDa
Source organism: Listeria monocytogenes EGD-e
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8Y8D7 (Residues: 1-264; Coverage: 100%)
Gene names: lmo0968, nadK1
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand GOL 1 x GOL
Ligand 5A8 4 x 5A8
Ligand CIT 1 x CIT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P21
Unit cell:
a: 66.92Å b: 119.34Å c: 67.75Å
α: 90° β: 100.37° γ: 90°
R-values:
R R work R free
0.226 0.224 0.259
Expression system: Escherichia coli

Quick links

Citations

1 review citation

NAD Kinases: Metabolic Targets Controlling Redox Co-enzymes and Reducing Power Partitioning in Plant Stress and Development.
Li et al. (2018)
4 other articles