SMTL ID : 9vdk.1

Cryo-EM structure of human ATP9A in BeF-bound E2P state open form

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.359, T.361, D.753, D.757 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.361, A:D.753, H2O.1, H2O.3

1 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

P5S.2: 12 residues within 4Å: Chain A: V.75, F.79, N.309, P.312, S.314, V.317, N.318, G.847, Y.848, T.850, M.854, F.858 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.75, A:F.79, A:V.317, A:F.858, A:F.858 Hydrogen bonds: A:N.309, A:S.314, A:S.314, A:G.847, A:T.850

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

PCW.3: 13 residues within 4Å: Chain A: V.325, W.328, V.329, F.855, F.858, S.859, L.862, H.945, W.946, L.947, A.951, L.954 Ligands: PCW.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.328, A:F.858, A:L.862, A:A.951, A:L.954 Salt bridges: A:H.945 PCW.4: 14 residues within 4Å: Chain A: I.86, R.87, V.90, R.94, K.323, I.324, S.327, W.328, R.331, R.332, T.339, V.340, S.344 Ligands: PCW.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.86, A:V.90, A:I.324, A:I.324, A:W.328 Salt bridges: A:R.94, A:R.94, A:R.331, A:R.331, A:R.331, A:R.332, A:R.332 PCW.6: 15 residues within 4Å: Chain A: K.46, Y.47, F.48, L.51, L.55, L.56, S.59, N.269, K.273, I.274, F.276, G.277, A.278, V.280, V.281 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.48, A:F.48, A:L.51, A:L.55, A:K.273, A:F.276, A:F.276, A:V.280, A:V.281 Hydrogen bonds: A:F.48, A:N.269 Salt bridges: A:K.273, A:K.273

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 7 residues within 4Å: Chain A: L.931, L.934, L.935, W.944, T.949, E.952, L.953 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.931, A:L.934, A:L.935, A:W.944, A:W.944, A:W.944, A:T.949, A:L.953

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abe, K. et al., A unique gating mechanism revealed by the cryo-EM structure of monomeric ATP9A flippase. J.Biol.Chem. (2025)

Release Date

2025-09-03

Peptides

Probable phospholipid-transporting ATPase IIA: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Probable phospholipid-transporting ATPase IIA

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