5YLV

Crystal structure of the gastric proton pump complexed with SCH28080


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of the gastric proton pump

Abe, K.Irie, K.Nakanishi, H.Suzuki, H.Fujiyoshi, Y.

(2018) Nature 556: 214-218

  • DOI: 10.1038/s41586-018-0003-8
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 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 steepes ...

    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.


    Organizational Affiliation

    CeSPIA Inc., Tokyo, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Potassium-transporting ATPase alpha chain 1A1034Sus scrofaMutation(s): 3 
Gene Names: ATP4A
EC: 3.6.3.10 (PDB Primary Data), 7.2.2.19 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
gastric H+,K+-ATPase with bound vonoprazan
Find proteins for P19156 (Sus scrofa)
Explore P19156 
Go to UniProtKB:  P19156
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Potassium-transporting ATPase subunit betaB289Sus scrofaMutation(s): 0 
Gene Names: ATP4B
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
gastric H+,K+-ATPase with bound vonoprazan
Find proteins for P18434 (Sus scrofa)
Explore P18434 
Go to UniProtKB:  P18434
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PCW
Query on PCW

Download CCD File 
B
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
 Ligand Interaction
CE1
Query on CE1

Download CCD File 
A, B
O-DODECANYL OCTAETHYLENE GLYCOL
C28 H58 O9
YYELLDKEOUKVIQ-UHFFFAOYSA-N
 Ligand Interaction
8WX
Query on 8WX

Download CCD File 
A
2-(2-methyl-8-phenylmethoxy-imidazo[1,2-a]pyridin-3-yl)ethanenitrile
C17 H15 N3 O
PYKJFEPAUKAXNN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
RB
Query on RB

Download CCD File 
A
RUBIDIUM ION
Rb
NCCSSGKUIKYAJD-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BFD
Query on BFD
AL-PEPTIDE LINKINGC4 H6 Be F3 N O4ASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.05α = 90
b = 105.05β = 90
c = 368.54γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary