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Crystal structure of NAD kinase 1 from Listeria monocytogenes in complexe with an adenine derivative

Analyse Crystal structure of NAD kinase 1 from Listeria monocytogenes in complexe with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RBS
Type: protein
Length: 261 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.324
Source: Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
Molecule: NAD kinase 1
EC: 2.7.1.23
UniProt: Q8Y8D7
Ligands: JXT
Pockets: 1 · best druggability 0.55

Structure

x-ray diffraction · resolution 2.324 · 1 distinct chain · 21% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NAD kinase 1 (EC 2.7.1.23)	protein	261	21% helix, 42% strand	Q8Y8D7

Ligands and binding sites

JXT · 8-bromanyl-9-pent-4-ynyl-purin-6-amine · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	113	0.55	0.83	23	CIT

Compared structures

6RBS · Crystal structure of NAD kinase 1 from listeria monocytogenes in complexe with an adenine… · 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 6RBS · PDBe 6RBS · UniProt Q8Y8D7

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