SMTL ID : 6k7m.1

Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2Pi-PL state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.1: 9 residues within 4Å: Chain A: W.333 Chain B: N.180, V.234, N.235, W.236, L.237, N.298, Y.299, P.300 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.300

1 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.2: 14 residues within 4Å: Chain A: D.194, G.195, E.196, D.414, K.415, T.416, L.674, T.675, G.676, K.771, D.791, N.794, D.795 Ligands: MG.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.414

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 9 residues within 4Å: Chain A: I.944, F.948, A.1051, L.1055 Chain B: F.324, I.327, A.328, A.331, I.335 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.324, B:F.324, B:I.327, B:A.328, B:A.331, B:I.335, B:I.335, A:I.944, A:F.948, A:L.1055

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 7 residues within 4Å: Chain A: G.195, D.414, T.416, D.791, G.792, D.795 Ligands: ALF.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.414, A:T.416, A:D.791

1 x D39: (2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid(Non-covalent)

D39.5: 15 residues within 4Å: Chain A: Q.93, T.105, T.106, P.109, F.112, N.357, N.358, I.362, S.363, V.366, T.367, V.370, Y.860, N.887, V.888 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.112, A:V.366, A:V.366, A:V.370 Hydrogen bonds: A:Q.93, A:T.106, A:N.357, A:N.358, A:N.358, A:I.362, A:S.363, A:Y.860, A:N.887

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

NAG.6: 4 residues within 4Å: Chain B: F.103, E.184, N.294, T.296 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.105 NAG.7: 1 residues within 4Å: Chain B: N.107 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hiraizumi, M. et al., Cryo-EM structures capture the transport cycle of the P4-ATPase flippase. Science (2019)

Release Date

2019-08-28

Peptides

Phospholipid-transporting ATPase: A
Cell cycle control protein 50A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Membrane

We predict this structure to be a membrane protein.
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Phospholipid-transporting ATPase

Cell cycle control protein 50A

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