› 3v8n

X-ray diffraction
2.38Å resolution

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 8-bromo-5'-amino-5'-deoxyadenosine, reacted with a citrate molecule in N site

Released:
DOI: 10.2210/pdb3v8n/pdb
PDB entry 3v8n coloured by chain, front view.
PDB entry 3v8n coloured by chain, side view.
PDB entry 3v8n coloured by chain, top view.
Source organism: Listeria monocytogenes
Primary publication:
Screening and in situ synthesis using crystals of a NAD kinase lead to a potent antistaphylococcal compound.
Gelin M, Poncet-Montange G, Assairi L, Morellato L, Huteau V, Dugué L, Dussurget O, Pochet S, Labesse G
Structure 20 1107-17 (2012)
PMID: 22608967

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 Chain: A
Molecule details ›
Chain: A
Length: 272 amino acids
Theoretical weight: 31.05 KDa
Source organism: Listeria monocytogenes
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 5NB 1 x 5NB
Ligand 5CI 1 x 5CI
Ligand CIT 1 x CIT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: I222
Unit cell:
a: 63.063Å b: 75.966Å c: 119.012Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.207 0.246
Expression system: Escherichia coli

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Citations

4 review citations

The ways and means of fragment-based drug design.
Doak et al. (2016)
3 more