SMTL ID : 6jxi.1

Rb+-bound E2-MgF state of the gastric proton pump (Tyr799Trp)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MF4: TETRAFLUOROMAGNESATE(2-)(Non-covalent)

MF4.1: 13 residues within 4Å: Chain A: T.182, G.183, E.184, D.339, K.340, T.341, T.580, G.581, D.582, K.661, D.680, N.683 Ligands: MG.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.339

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

PCW.2: 10 residues within 4Å: Chain A: Q.838, Q.950, L.953, V.954, P.957, L.960 Chain B: I.53, L.56, C.57, T.64 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.953, A:P.957 Hydrogen bonds: A:Q.838 PCW.4: 9 residues within 4Å: Chain A: F.265, T.751, I.755, T.758, L.844, V.847, Q.852 Ligands: PCW.12, PCW.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.265, A:T.751, A:I.755, A:L.844 PCW.12: 7 residues within 4Å: Chain A: I.271, V.272, C.275, I.276, G.277, T.758 Ligands: PCW.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.271, A:V.272, A:V.272, A:I.276, A:I.276 PCW.15: 16 residues within 4Å: Chain A: T.751, A.822, S.825, F.826, F.829, F.833, P.843, L.844 Chain B: S.51, F.54, A.55, Y.59, M.62, I.65 Ligands: PCW.4, CLR.16 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.751, A:A.822, A:F.826, A:F.826, A:F.829, A:F.829, A:F.833, A:P.843, A:L.844, B:F.54, B:Y.59

1 x CE1: O-DODECANYL OCTAETHYLENE GLYCOL(Non-covalent)

CE1.3: 9 residues within 4Å: Chain A: I.894, Y.934, P.946, I.947, R.948, F.949, W.952, L.960, F.963 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.963

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: D.339, T.341, D.680 Ligands: MF4.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.339, A:T.341, A:D.680, H2O.3, H2O.4

6 x RB: RUBIDIUM ION(Non-covalent)

RB.6: 3 residues within 4Å: Chain A: D.680, A.700, S.702 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.680, A:A.700 RB.7: 3 residues within 4Å: Chain A: V.410, G.412, T.417 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.410, H2O.5 RB.8: 5 residues within 4Å: Chain A: L.688, K.689, A.691, D.710 Ligands: RB.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.689, A:A.691, A:D.710, H2O.3 RB.9: 5 residues within 4Å: Chain A: E.243, K.689, K.690, A.691 Ligands: RB.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:K.689 RB.10: 3 residues within 4Å: Chain A: L.458, D.460, D.463 No protein-ligand interaction detected (PLIP) RB.11: 8 residues within 4Å: Chain A: V.292, A.293, V.295, E.297, N.746, E.749, I.770, E.774 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:A.293, A:V.295, A:E.297, A:E.749

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

NAG.13: 5 residues within 4Å: Chain B: N.98, S.100, N.254, Q.288, K.289 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.288 Hydrogen bonds: B:K.289 NAG.14: 3 residues within 4Å: Chain B: N.160, E.215, L.249 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.249 Hydrogen bonds: B:N.160, B:E.215 NAG.17: 1 residues within 4Å: Chain B: N.220 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.220 NAG.18: 1 residues within 4Å: Chain B: N.192 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.192 NAG.19: 2 residues within 4Å: Chain B: N.145, H.238 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.145

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.16: 9 residues within 4Å: Chain A: E.810, A.814, F.818 Chain B: R.31, W.36, I.39, Y.43, Y.47 Ligands: PCW.15 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.39, B:Y.43, B:Y.43, B:Y.47, A:A.814, A:F.818 Hydrogen bonds: B:R.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamamoto, K. et al., A single K + -binding site in the crystal structure of the gastric proton pump. Elife (2019)

Release Date

2019-08-14

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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