Crystal structure of the gastric proton pump K791S/E820D/Y340N in (BYK)E2BEF state

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).

Ligands and binding sites

• J3C · (7R,8R,9S)-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridine-7,8-diol · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B
• RB · Rubidium ion · metal · 3 copies · chains A
• MG · Magnesium ion · metal · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1993 Ų buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 glycan, 2 disulfide, 1 modified (N-glycosylation, disulfide, nonstandard).

Compared structures

• 7EFM · Crystal structure of the gastric proton pump K791S/E820D/Y340N in (BYK)E2BeF state · 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

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 A0A5G2QYH2
• Every structure of UniProt P18434
• Elsewhere: RCSB PDB 7EFM · PDBe 7EFM · UniProt A0A5G2QYH2 · UniProt P18434