SMTL ID : 8wa5.1

Cryo-EM structure of the gastric proton pump Y799W/E936Q mutant in K+-occluded (K+)E2-AlF state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

3 x K: POTASSIUM ION(Non-covalent)

K.1: 8 residues within 4Å: Chain A: V.338, A.339, V.341, E.343, N.792, E.795, I.816, E.820 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.339, A:V.341, A:E.795 K.2: 4 residues within 4Å: Chain A: L.734, K.735, A.737, D.756 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:L.734, A:K.735, A:A.737 K.3: 3 residues within 4Å: Chain A: K.735, K.736, A.737 No protein-ligand interaction detected (PLIP)

1 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.4: 13 residues within 4Å: Chain A: T.228, G.229, E.230, D.385, K.386, T.387, T.626, G.627, K.707, D.726, N.729, D.730 Ligands: MG.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.385

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: D.385, T.387, D.726, D.730 Ligands: ALF.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.385, A:T.387, A:D.726

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 7 residues within 4Å: Chain A: E.856, A.860, F.864 Chain B: W.37, Y.44, Y.48 Ligands: PCW.7 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.37, B:Y.44, B:Y.48, A:A.860, A:F.864 Hydrogen bonds: B:R.32, A:E.856, A:E.856

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

PCW.7: 19 residues within 4Å: Chain A: T.797, A.868, S.871, F.872, F.875, F.879, F.888, P.889, L.890, V.893 Chain B: Y.48, S.52, F.55, A.56, Y.60, M.63, I.66, P.68 Ligands: CLR.6 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:Y.48, B:Y.48, B:F.55, B:A.56, A:T.797, A:A.868, A:F.872, A:F.872, A:F.872, A:F.875, A:P.889, A:L.890, A:V.893

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

NAG.8: 5 residues within 4Å: Chain B: N.99, S.101, D.102, Q.289, K.290 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.99 NAG.9: 2 residues within 4Å: Chain B: N.161, K.248 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.161 NAG.10: 2 residues within 4Å: Chain B: A.220, N.221 No protein-ligand interaction detected (PLIP) NAG.11: 1 residues within 4Å: Chain B: N.193 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain B: P.145, N.146 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Madapally, H.V. et al., Specific protonation of acidic residues confers K + selectivity to the gastric proton pump. J.Biol.Chem. (2023)

Release Date

2023-11-29

Peptides

Sodium/potassium-transporting ATPase subunit alpha: 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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Sodium/potassium-transporting ATPase subunit alpha

Potassium-transporting ATPase subunit beta

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