Crystal structure of NAD kinase 1 from listeria monocytogenes in complex with a new di-adenosine inhibitor formed in situ

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 41% strand (DSSP).

Ligands and binding sites

• ZNB · 2-[6-azanyl-9-[(2R,3R,4S,5R)-5-[[(azanylidene-$l^{4}-azanylidene)amino]methyl]-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]sulfanyl-N-[[(2R,3S,4R,5R)-5-(6-azanyl-8-bromanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]ethanamide · ligand · chains A
• CIT · Citric acid · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Compared structures

• 3V8P · Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a new… · the same entry in another collection · chain A against A, TM-score 1.00
• Q8Y8D7 · AlphaFold monomer V2.0 prediction for NAD kinase 1 (Q8Y8D7) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q8Y8D7
• Elsewhere: RCSB PDB 3V8P · PDBe 3V8P · UniProt Q8Y8D7