MolNFT v1 · #171470 · protein

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

6Z64: “Crystal structure of NAD kinase 1 from listeria monocytogenes in complex with a di-adenosine derivative”. X-ray diffraction, 1 ligand (Q9K), 1 pocket (best druggability 0.58). MolNFT v1 #171470 on GenesisL1: 3D structure, binding…

PDB: 6Z64
Type: protein
Length: 262 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD kinase 1
EC: 2.7.1.23
UniProt: Q8Y8D7
Ligands: Q9K
Pockets: 1 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NAD kinase 1 (EC 2.7.1.23)	protein	262	23% helix, 43% strand	Q8Y8D7

Ligands and binding sites

Q9K · (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]prop-2-ynyl-(3-azanylpropyl)amino]methyl]oxolane-3, 4-diol · 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	117	0.58	0.84	24	CIT

Compared structures

6Z64 · Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00

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 6Z64 · PDBe 6Z64 · UniProt Q8Y8D7

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