SMTL ID : 7bsq.1

Cryo-EM structure of a human ATP11C-CDC50A flippase in E1AlF-ADP state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.1: 8 residues within 4Å: Chain A: W.316 Chain B: N.180, V.234, N.235, W.236, L.237, N.298, P.300 No protein-ligand interaction detected (PLIP)

1 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.2: 8 residues within 4Å: Chain A: D.402, T.404, T.667, G.668, K.788, N.812, D.813 Ligands: ADP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.402, A:D.402

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)

ADP.3: 20 residues within 4Å: Chain A: D.402, T.404, S.488, D.490, E.491, F.533, A.535, R.538, M.540, K.556, G.557, A.558, R.587, L.589, G.668, D.669, R.782, N.812 Ligands: ALF.2, MG.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:T.404, A:S.488, A:S.488, A:E.491, A:R.587, A:D.669, A:D.669, A:D.669, A:R.782, A:R.782, A:N.812 Salt bridges: A:R.587 pi-Stacking: A:F.533, A:F.533

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: T.406, I.807, G.808, D.809, I.826 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:I.807 MG.5: 2 residues within 4Å: Chain A: E.830 Ligands: ADP.3 No protein-ligand interaction detected (PLIP)

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

NAG.6: 3 residues within 4Å: Chain B: T.105, F.186, N.294 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.184 NAG.7: 4 residues within 4Å: Chain B: N.107, I.188, R.290, W.292 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.292 Hydrogen bonds: B:N.107, B:R.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakanishi, H. et al., Transport Cycle of Plasma Membrane Flippase ATP11C by Cryo-EM. Cell Rep (2020)

Release Date

2020-09-30

Peptides

ATP11C: A
CDC50A: 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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ATP11C

CDC50A

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