SMTL ID : 9kck.1

Cryo-EM structure of human sodium pump E1003K in (2K+)E2-AlF state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.1: 13 residues within 4Å: Chain A: T.181, G.182, E.183, D.338, K.339, T.340, T.579, G.580, K.660, D.679, N.682, D.683 Ligands: MG.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.338, A:D.338

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.338, T.340, D.679 Ligands: ALF.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.338, A:T.340, A:D.679, H2O.1, H2O.1

3 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: T.741, S.744, N.745, D.773, D.777 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.741, A:S.744, A:D.773 K.4: 8 residues within 4Å: Chain A: V.291, A.292, V.294, E.296, N.745, E.748, I.769, D.773 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:V.291, A:A.292, A:V.294, A:E.748, A:D.773 K.5: 4 residues within 4Å: Chain A: L.687, K.688, A.690, D.709 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:L.687, A:A.690

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 6 residues within 4Å: Chain A: S.813, M.821 Chain B: R.31, W.36, Y.43, Y.47 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.36, B:Y.43, B:Y.43 Hydrogen bonds: B:R.31, B:R.31

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

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-1

Sodium/potassium-transporting ATPase subunit beta-3

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