SMTL ID : 8oxa.1

Cryo-EM structure of ATP8B1-CDC50A in E2-Pi conformation with occluded PS

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 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.304, A:W.371

1 x VN4: oxido(dioxo)vanadium(Non-covalent)

VN4.2: 11 residues within 4Å: Chain A: G.233, E.234, D.454, K.455, T.456, T.732, G.733, K.873, N.896, D.897 Ligands: MG.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.233, A:K.455, A:T.456, A:G.733, A:K.873, A:N.896, A:D.897

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.454, T.456, D.893 Ligands: VN4.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.454, A:T.456, A:D.893

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)

D39.4: 18 residues within 4Å: Chain A: Q.131, T.143, T.144, P.147, N.397, P.401, I.402, S.403, V.406, V.410, N.989, V.990, L.991, S.994, L.995, F.1101, G.1105, L.1109 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.406, A:V.410, A:L.995, A:F.1101, A:F.1101, A:L.1109 Hydrogen bonds: A:Q.131, A:T.143, A:T.144, A:I.402, A:S.403, A:N.989 Water bridges: A:I.985, A:N.989

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

NAG.5: 1 residues within 4Å: Chain B: N.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.111 NAG.6: 3 residues within 4Å: Chain B: F.107, T.109, N.298 No protein-ligand interaction detected (PLIP)

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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