SMTL ID : 6jxh.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.339

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: G.183, 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.1, H2O.6

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

PCW.3: 14 residues within 4Å: Chain A: Q.838, F.949, Q.950, L.953, V.954, P.957, L.960, L.961, V.964 Chain B: I.53, L.56, C.57, T.64, Y.72 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.953, A:P.957, A:P.957, A:L.960, A:L.960, A:V.964 Hydrogen bonds: A:Q.838 PCW.4: 7 residues within 4Å: Chain A: F.265, T.751, I.755, T.758, V.847 Ligands: PCW.5, PCW.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.265, A:T.751, A:V.847 PCW.5: 10 residues within 4Å: Chain A: T.268, F.269, I.271, V.272, I.276, G.277, T.758, S.760, R.850 Ligands: PCW.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.269, A:I.271, A:V.272, A:V.272, A:V.272, A:I.276, A:T.758 Hydrogen bonds: A:R.850 PCW.13: 17 residues within 4Å: Chain A: I.755, A.822, S.825, F.826, F.829, F.833, P.843, L.844 Chain B: Y.47, S.51, A.55, I.58, Y.59, M.62, I.65 Ligands: PCW.4, CLR.14 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.755, A:A.822, A:F.826, A:F.826, A:F.829, A:F.829, A:P.843, A:L.844, B:Y.47, B:I.58

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

CE1.6: 12 residues within 4Å: Chain A: M.891, I.894, Y.934, P.946, I.947, R.948, F.949, W.952, M.956, S.959, L.960, F.963 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.894, A:F.963

6 x K: POTASSIUM ION(Non-covalent)

K.7: 2 residues within 4Å: Chain A: D.680, A.700 No protein-ligand interaction detected (PLIP) K.8: 3 residues within 4Å: Chain A: V.410, G.412, T.417 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.410, H2O.10, H2O.12 K.9: 4 residues within 4Å: Chain A: L.688, K.689, A.691, D.710 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:K.689, A:A.691, A:D.710 K.10: 4 residues within 4Å: Chain A: E.243, K.689, K.690, A.691 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:K.689, H2O.6, H2O.9 K.11: 4 residues within 4Å: Chain A: T.457, L.458, D.460, D.463 No protein-ligand interaction detected (PLIP) K.12: 8 residues within 4Å: Chain A: V.292, A.293, V.295, E.297, N.746, E.749, I.770, E.774 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:V.292, A:A.293, A:V.295, A:E.297, A:E.749

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.14: 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.13 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.36, B:I.39, B:Y.43, B:Y.43, B:Y.47, A:A.814, A:F.818 Hydrogen bonds: B:R.31

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.15: 4 residues within 4Å: Chain B: N.98, S.100, Q.288, K.289 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.288 Hydrogen bonds: B:K.289 NAG.16: 1 residues within 4Å: Chain B: N.129 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.129 NAG.17: 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.18: 1 residues within 4Å: Chain B: N.220 No protein-ligand interaction detected (PLIP) NAG.19: 1 residues within 4Å: Chain B: N.192 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.192 NAG.20: 3 residues within 4Å: Chain B: P.144, N.145, H.238 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.145

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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