SMTL ID : 9kcg.1

Cryo-EM structure of human sodium pump WT in (3Na+)E1-AMPPCP state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: V.291, A.292, V.294, E.296, D.773 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.291, A:E.296 Water bridges: A:G.297 NA.2: 6 residues within 4Å: Chain A: A.292, N.293, T.741, S.744, N.745, D.777 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.741 Water bridges: A:N.745, A:D.773 NA.3: 6 residues within 4Å: Chain A: Y.740, T.741, T.743, S.744, D.777, Q.892 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.743, A:S.744

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: D.338, D.679, G.680, N.682, D.683 Ligands: ACP.6 No protein-ligand interaction detected (PLIP)

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 10 residues within 4Å: Chain A: F.829, E.837, T.948, F.951, C.952, P.955 Chain B: L.53, T.57, V.60, M.61 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.53, B:T.57, B:V.60, B:M.61, A:F.829 Hydrogen bonds: A:T.948 CLR.8: 10 residues within 4Å: Chain A: W.893, T.924, Y.932, P.947, W.950, F.951 Chain C: L.142, R.145, V.149, L.153 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:W.893, A:P.947, A:W.950, A:W.950, A:F.951, C:L.142, C:R.145, C:V.149, C:V.149, C:L.153 Hydrogen bonds: C:R.145 CLR.12: 9 residues within 4Å: Chain A: L.753, I.757, I.812, S.813, M.821 Chain B: Y.43, Y.47 Ligands: PC1.7, PCW.10 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.753, A:I.757, A:I.812, B:Y.43

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.6: 21 residues within 4Å: Chain A: D.338, K.339, T.340, S.414, E.415, F.444, S.446, K.449, Q.451, K.470, G.471, R.513, V.514, L.515, T.579, G.580, D.581, R.654, T.655, K.660 Ligands: MG.4 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:D.338, A:D.338, A:D.338, A:K.339, A:T.340, A:T.340, A:S.414, A:E.415, A:E.415, A:K.470, A:R.513, A:T.579, A:G.580, A:G.580, A:D.581, A:D.581, A:R.654, A:K.660, A:N.682 Salt bridges: A:K.449, A:K.660 pi-Stacking: A:F.444, A:F.444

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.7: 13 residues within 4Å: Chain A: F.253, I.256, I.749, L.753, K.805, V.807, N.808, E.809, I.812, Y.816 Chain B: L.29 Ligands: PC1.11, CLR.12 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.256, A:I.749, A:I.812, A:I.812, A:Y.816 Hydrogen bonds: A:E.809 Salt bridges: A:E.809 PC1.11: 10 residues within 4Å: Chain A: H.252, I.256, F.263, L.264, S.267, L.271, L.753 Chain B: W.16, F.19 Ligands: PC1.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.263, A:F.263, A:L.264, A:L.264, A:L.271, A:L.753 Salt bridges: A:H.252

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

PCW.9: 16 residues within 4Å: Chain A: W.51, V.97, V.101, I.104, T.105, F.108, Y.111, K.311, R.315, L.774, M.778, V.779, I.782, Y.786, I.915 Chain C: L.161 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.51, A:V.97, A:F.108, A:F.108, A:F.108, A:Y.111, A:M.778, A:V.779, A:I.782, A:I.782 PCW.10: 19 residues within 4Å: Chain A: T.750, L.825, F.828, F.832, L.841, P.842, I.843, L.846 Chain B: Y.47, A.51, F.54, S.55, M.58, W.59, L.62, Q.63, L.65, D.67 Ligands: CLR.12 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:T.750, A:L.825, A:F.828, A:F.828, A:F.832, A:P.842, A:I.843, A:L.846, B:Y.47, B:Y.47, B:A.51, B:F.54 Salt bridges: B:D.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dou, Y. et al., Structural basis of a sodium pump quaternary complex leading phospholipid scrambling in the living cell. To Be Published

Release Date

2025-11-12

Peptides

Sodium/potassium-transporting ATPase subunit alpha-1: A
Sodium/potassium-transporting ATPase subunit beta-3: B
FXYD domain-containing ion transport regulator 5: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Sodium/potassium-transporting ATPase subunit alpha-1

Sodium/potassium-transporting ATPase subunit beta-3

FXYD domain-containing ion transport regulator 5

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