SMTL ID : 8ox9.1

Cryo-EM structure of ATP8B1-CDC50A in E2P active conformation with bound PC

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

NAG-NAG-BMA.1: 8 residues within 4Å: Chain A: W.371 Chain B: N.184, V.238, N.239, L.241, N.302, Y.303, P.304 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.304, A:W.371 Hydrogen bonds: B:N.239

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)

BEF.2: 10 residues within 4Å: Chain A: G.233, D.454, K.455, T.456, T.732, G.733, K.873, D.893, N.896 Ligands: MG.3 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.454, T.456, D.893 Ligands: BEF.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.454, A:T.456, A:D.893

1 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.4: 19 residues within 4Å: Chain A: P.147, N.397, T.398, P.401, I.402, S.403, V.406, S.407, T.986, L.987, N.989, V.990, L.991, S.994, L.995, F.1101, G.1105, S.1106, L.1109 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.147, A:V.406, A:L.987, A:L.995, A:F.1101, A:L.1109 Hydrogen bonds: A:I.402, A:S.403, A:N.989 Water bridges: A:S.403

1 x IP9: (2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dioctanoate(Non-covalent)

IP9.5: 12 residues within 4Å: Chain A: R.1032, V.1035, H.1039, L.1042, I.1046, V.1155, P.1159, V.1160, I.1163, R.1164, S.1167, W.1171 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.1042, A:I.1046, A:P.1159, A:I.1163 Hydrogen bonds: A:R.1164, A:S.1167 Salt bridges: A:R.1032, A:R.1032, A:H.1039, A:H.1039, A:R.1164

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

NAG.6: 2 residues within 4Å: Chain B: N.111, I.192 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.111 NAG.7: 4 residues within 4Å: Chain B: F.107, T.109, E.188, N.298 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dieudonne, T. et al., Activation and substrate specificity of the human P4-ATPase ATP8B1. Nat Commun (2023)

Release Date

2023-11-29

Peptides

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

Cell cycle control protein 50A

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