MolNFT v1 · #171234 · protein

Crystal structure of the ADP-bound form of choline kinase from plasmodium falciparum

6YXT: “Crystal structure of the ADP-bound form of choline kinase from plasmodium falciparum”. X-ray diffraction, 2 ligands (ADP, MG), 5 pockets (best druggability 0.76). MolNFT v1 #171234 on GenesisL1: 3D structure, binding sites and…

PDB: 6YXT
Type: protein
Length: 359 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Choline kinase
EC: 2.7.1.32
UniProt: Q8IM71
Ligands: ADP, MG
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Choline kinase (EC 2.7.1.32)	protein	359	49% helix, 14% strand	Q8IM71

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · 2 copies · chains A
EDO · 1,2-ethanediol · additive · 3 copies · chains A

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	616	0.76	0.82	53	MG, ADP, EDO
2	105	0.53	0.83	22	empty
3	87	0.47	0.82	17	empty
4	95	0.46	0.80	12	EDO
5	130	0.45	0.76	16	EDO

Compared structures

6YXT · Crystal structure of the ADP-bound form of choline kinase from Plasmodium falciparum · 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 Q8IM71
Elsewhere: RCSB PDB 6YXT · PDBe 6YXT · UniProt Q8IM71

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