SMTL ID : 7w4a.1

Cryo-EM structure of the gastric proton pump complexed with revaprazan

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x 8CK: N-(4-fluorophenyl)-4,5-dimethyl-6-[(1R)-1-methyl-3,4-dihydro-1H-isoquinolin-2-yl]pyrimidin-2-amine(Non-covalent)

8CK.1: 13 residues within 4Å: Chain A: A.124, D.138, N.139, L.142, V.332, M.335, A.336, A.340, E.796, Y.800, L.810, C.814, I.817 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.124, A:V.332, A:A.336, A:A.336, A:A.340, A:E.796, A:Y.800, A:L.810, A:I.817, A:I.817 Hydrogen bonds: A:D.138 Water bridges: A:Q.128

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 2 residues within 4Å: Chain A: N.289, D.757 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.289

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.386, T.388, D.727, D.731 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.388, A:D.727

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 6 residues within 4Å: Chain B: N.99, S.101, D.102, N.255, Q.289, K.290 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.289 Hydrogen bonds: B:Q.289, B:K.290, B:K.290 NAG.5: 2 residues within 4Å: Chain B: N.130, K.153 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.130 NAG.6: 2 residues within 4Å: Chain B: N.161, K.248 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.248

1 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PCW.7: 12 residues within 4Å: Chain A: I.794, T.798, A.869, F.873, F.876, F.880, P.890, L.891 Chain B: S.52, F.55, A.56, M.63 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.794, A:A.869, A:F.873, A:F.873, A:F.876, A:F.880, B:F.55, B:A.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, S. et al., Structural Basis for Binding of Potassium-Competitive Acid Blockers to the Gastric Proton Pump. J.Med.Chem. (2022)

Release Date

2022-03-02

Peptides

Potassium-transporting ATPase alpha chain 1: A
Potassium-transporting ATPase subunit beta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Potassium-transporting ATPase alpha chain 1

Potassium-transporting ATPase subunit beta

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