Crystal structure of the ATP-gated human P2X3 ion channel bound to agonist 2-methylthio-ATP in the desensitized state

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 40% strand (DSSP).

Ligands and binding sites

• 6AT · 2-(methylsulfanyl)adenosine 5'-(tetrahydrogen triphosphate) · ligand · chains A
• ATP · Adenosine-5'-triphosphate · ligand · chains B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
• NA · Sodium ion · metal · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 30 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

• 5SVM · Crystal structure of the ATP-gated human P2X3 ion channel bound to agonist… · the same entry in another collection · chain A against A, TM-score 1.00
• P56373 · AlphaFold monomer V2.0 prediction for P2X purinoceptor 3 (P56373) · a predicted model of the same protein · chain B 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 P56373
• Elsewhere: RCSB PDB 5SVM · PDBe 5SVM · UniProt P56373