› 7zze

X-ray diffraction
1.78Å resolution

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a linear di-adenosine derivative

Released:
DOI: 10.2210/pdb7zze/pdb
PDB entry 7zze coloured by chain, front view.
PDB entry 7zze coloured by chain, side view.
PDB entry 7zze coloured by chain, top view.
Source organism: Listeria monocytogenes EGD-e
Primary publication:
Synthesis and structure-activity relationship studies of original cyclic diadenosine derivatives as nanomolar inhibitors of NAD kinase from pathogenic bacteria.
Clément DA, Gelin M, Leseigneur C, Huteau V, Mondange L, Pons JL, Dussurget O, Lionne C, Labesse G, Pochet S
Eur J Med Chem 246 114941 (2023)
PMID: 36455355

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-186998 (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 EGD-e
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8Y8D7 (Residues: 1-264; Coverage: 100%)
Gene names: lmo0968, nadK1
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand CIT 1 x CIT
Ligand OVL 1 x OVL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-1
Spacegroup: I222
Unit cell:
a: 63.134Å b: 74.526Å c: 118.438Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.24
Expression system: Escherichia coli BL21(DE3)

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