SMTL ID : 7et1.1

Cryo-EM structure of the gastric proton pump K791S/E820D/Y340N/E936V/Y799W mutant in K+-occluded (K+)E2-AlF state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.339, T.341, D.680, D.684 Ligands: ALF.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.339, A:T.341, A:D.680

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

PCW.2: 9 residues within 4Å: Chain A: F.269, I.747, T.758, F.818, V.847, G.848, Q.852 Ligands: PCW.3, PCW.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.269, A:I.747, A:T.758, A:F.818, A:V.847 PCW.3: 14 residues within 4Å: Chain A: T.268, F.269, I.271, V.272, C.275, I.276, G.277, Y.278, I.757, T.758, S.760, R.850, P.851 Ligands: PCW.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.268, A:F.269, A:F.269, A:I.271, A:I.271, A:V.272, A:I.276, A:Y.278, A:T.758 Hydrogen bonds: A:R.850 PCW.9: 15 residues within 4Å: Chain A: T.751, S.825, F.829, F.842, P.843, L.844 Chain B: Y.20, S.24, F.27, A.28, I.31, M.35, I.38, P.40 Ligands: PCW.2 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.20, B:F.27, B:F.27, B:A.28, A:F.829, A:P.843, A:L.844

3 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: L.688, K.689, A.691, G.694, D.710 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:L.688, A:A.691, A:D.710 K.7: 6 residues within 4Å: Chain A: T.742, S.745, N.746, E.749, D.774, D.778 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.745, A:D.774 K.8: 7 residues within 4Å: Chain A: V.292, A.293, V.295, E.297, N.746, E.749, D.774 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:A.293, A:V.295, A:E.749, A:D.774

1 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.5: 12 residues within 4Å: Chain A: T.182, G.183, D.339, K.340, T.341, T.580, G.581, K.661, D.680, N.683, D.684 Ligands: MG.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.339, A:D.339, H2O.1

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 6 residues within 4Å: Chain A: E.810, F.818 Chain B: W.9, I.12, Y.16, V.17 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.818, B:W.9, B:I.12, B:Y.16, B:Y.16, B:Y.16, B:V.17 Hydrogen bonds: A:E.810

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

NAG.10: 6 residues within 4Å: Chain B: N.71, S.73, D.74, N.227, Q.261, K.262 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.261 Hydrogen bonds: B:K.262 NAG.11: 4 residues within 4Å: Chain B: N.133, E.188, K.220, L.222 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.222 Hydrogen bonds: B:K.220 NAG.12: 2 residues within 4Å: Chain B: A.192, N.193 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.193 NAG.13: 1 residues within 4Å: Chain B: N.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.165 NAG.14: 2 residues within 4Å: Chain B: P.117, N.118 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abe, K. et al., Gastric proton pump with two occluded K + engineered with sodium pump-mimetic mutations. Nat Commun (2021)

Release Date

2021-09-01

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