5YLU

Crystal structure of the gastric proton pump complexed with vonoprazan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79989 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The gastric proton pump-the H <sup>+ </sup>, K <sup>+ </sup>-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

    Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY, USA.,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan.,Japan Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Nagoya, Japan.,Japan Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Nagoya, Japan. kabe@cespi.nagoya-u.ac.jp.,Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan. kabe@cespi.nagoya-u.ac.jp.,Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan. kabe@cespi.nagoya-u.ac.jp.,CeSPIA Inc., Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Potassium-transporting ATPase alpha chain 1
A
1034Sus scrofaMutation(s): 3 
Gene Names: ATP4A
EC: 7.2.2.19
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
gastric H+,K+-ATPase with bound BeF and SCH28080
Find proteins for P19156 (Sus scrofa)
Go to Gene View: ATP4A
Go to UniProtKB:  P19156
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Potassium-transporting ATPase subunit beta
B
289Sus scrofaMutation(s): 0 
Gene Names: ATP4B
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
gastric H+,K+-ATPase with bound BeF and SCH28080
Find proteins for P18434 (Sus scrofa)
Go to Gene View: ATP4B
Go to UniProtKB:  P18434
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CE1
Query on CE1

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

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HKT
Query on HKT

Download SDF File 
Download CCD File 
A
1-[5-(2-fluorophenyl)-1-pyridin-3-ylsulfonyl-pyrrol-3-yl]-~{N}-methyl-methanamine
Vonoprazan
C17 H16 F N3 O2 S
BFDBKMOZYNOTPK-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PCW
Query on PCW

Download SDF File 
Download CCD File 
A
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
(Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BFD
Query on BFD
A
L-PEPTIDE LINKINGC4 H6 Be F3 N O4ASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79989 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.237 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 104.820α = 90.00
b = 104.820β = 90.00
c = 367.080γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
phenix.refinerefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references