Crystal structure of the gastric proton pump complexed with vonoprazan

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).

Ligands and binding sites

• PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A, B
• CE1 · O-dodecanyl octaethylene glycol · ligand · 2 copies · chains A, B
• HKT · 1-[5-(2-fluorophenyl)-1-pyridin-3-ylsulfonyl-pyrrol-3-yl]-~{N}-methyl-methanamine · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B
• MG · Magnesium ion · metal · chains A

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

Pockets

18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1885 Ų buried · 30 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 3 glycan, 1 modified (disulfide, N-glycosylation, nonstandard).

Compared structures

• 5YLU · Crystal structure of the gastric proton pump complexed with vonoprazan · the same entry in another collection · chain A against A, TM-score 1.00
• P18434 · AlphaFold monomer V2.0 prediction for potassium-transporting ATPase subunit beta (P18434) · a predicted model of the same protein · chain B against A, TM-score 0.96
• P19156 · AlphaFold monomer V2.0 prediction for potassium-transporting ATPase alpha chain 1 (P19156) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P19156
• Every structure of UniProt P18434
• Elsewhere: RCSB PDB 5YLU · PDBe 5YLU · UniProt P19156 · UniProt P18434