5YLU image
Entry Detail
PDB ID:
5YLU
Title:
Crystal structure of the gastric proton pump complexed with vonoprazan
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2017-10-19
Release Date:
2018-04-11
Method Details:
Experimental Method:
Resolution:
2.80 Å
R-Value Free:
0.28
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 31 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Potassium-transporting ATPase alpha chain 1
Mutations:R220C, S593C, G1005S
Chain IDs:A
Chain Length:1034
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Description:Potassium-transporting ATPase subunit beta
Chain IDs:B
Chain Length:289
Number of Molecules:1
Biological Source:Sus scrofa
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
BFD A ASP modified residue
Primary Citation
Crystal structures of the gastric proton pump
Nature 556 214 218 (2018)
PMID: 29618813 DOI: 10.1038/s41586-018-0003-8

Abstact

The gastric proton pump-the H+, K+-ATPase-is a P-type ATPase responsible for acidifying the gastric juice down to pH 1. This corresponds to a million-fold proton gradient across the membrane of the parietal cell, the steepest known cation gradient of any mammalian tissue. The H+, K+-ATPase is an important target for drugs that treat gastric acid-related diseases. Here we present crystal structures of the H+, K+-ATPase in complex with two blockers, vonoprazan and SCH28080, in the luminal-open state, at 2.8 Å resolution. The drugs have partially overlapping but clearly distinct binding modes in the middle of a conduit running from the gastric lumen to the cation-binding site. The crystal structures suggest that the tight configuration at the cation-binding site lowers the pK a value of Glu820 sufficiently to enable the release of a proton even into the pH 1 environment of the stomach.

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Primary Citation of related structures