SMTL ID : 8ijm.1

Cyo-EM structure of K794A non-gastric proton pump in Na+ bound E1AMPPCP state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Covalent)

ACP.1: 17 residues within 4Å: Chain A: D.338, K.339, T.340, D.412, S.414, E.415, F.444, Q.451, K.470, G.471, A.472, R.513, V.514, L.515, V.578, G.580, D.581 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:D.338, A:D.338, A:K.339, A:T.340, A:S.414, A:Q.451, A:Q.451, A:K.470, A:R.513, A:G.580 Salt bridges: A:R.513 pi-Stacking: A:F.444, A:F.444

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

PCW.2: 7 residues within 4Å: Chain A: Q.837, Q.949, F.952, P.956 Chain B: T.73, T.87, Y.88 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Q.949, A:P.956, B:T.73 Hydrogen bonds: A:Q.837 PCW.3: 15 residues within 4Å: Chain A: C.750, I.754, L.760, L.825, F.828, F.832, W.841, P.842, T.843 Chain B: A.67, F.70, I.74, Q.75, L.78, I.81 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.754, A:L.760, A:F.828, A:F.832, A:P.842, A:T.843, B:A.67, B:F.70, B:I.74 Hydrogen bonds: A:T.843, A:T.843, A:T.843, B:Q.75 pi-Cation interactions: A:W.841, A:W.841

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.4: 7 residues within 4Å: Chain A: T.809, I.813 Chain B: W.52, I.55, L.56, Y.59, Y.63 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.52, B:W.52, B:I.55, B:L.56, B:Y.59, B:Y.63

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

NA.5: 7 residues within 4Å: Chain A: A.292, T.741, A.744, N.745, D.773, D.777 Ligands: NA.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.741, A:N.745 NA.6: 6 residues within 4Å: Chain A: Y.740, T.741, A.744, D.777, Q.892 Ligands: NA.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.740, A:A.744, A:D.777, A:Q.892

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

NAG.7: 1 residues within 4Å: Chain B: N.178 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abe, K. et al., An unusual conformation from Na + -sensitive non-gastric proton pump mutants reveals molecular mechanisms of cooperative Na + -binding. Biochim Biophys Acta Mol Cell Res (2023)

Release Date

2023-08-02

Peptides

Sodium/potassium-transporting ATPase subunit alpha: A
Sodium/potassium-transporting ATPase subunit beta-1: 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

Sodium/potassium-transporting ATPase subunit beta-1

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