SMTL ID : 7bsu.1

Cryo-EM structure of a human ATP11C-CDC50A flippase in PtdSer-bound E2BeF state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: A.169, D.402, T.404, D.809 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.404, A:D.809

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

P5S.2: 30 residues within 4Å: Chain A: F.65, V.82, T.83, L.86, P.87, F.90, N.345, F.346, I.348, V.350, S.351, V.354, T.355, M.358, A.898, A.899, T.902, M.903, N.905, I.906, C.907, S.910, L.911, F.1017, V.1018, G.1021, S.1022, F.1025, F.1029, W.1033 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.899, A:T.902, A:L.911, A:F.1017, A:F.1017 Hydrogen bonds: A:N.345, A:N.345, A:N.345, A:N.905

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

NAG.3: 5 residues within 4Å: Chain B: N.180, N.235, L.237, N.298 Ligands: NAG.4 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.237 Hydrogen bonds: B:N.180 NAG.4: 7 residues within 4Å: Chain A: W.316 Chain B: V.234, N.235, P.300, Y.303 Ligands: NAG.3, AH2.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.316 NAG.6: 5 residues within 4Å: Chain B: T.105, F.186, P.194, W.292, N.294 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.194, B:W.292 NAG.7: 3 residues within 4Å: Chain B: N.107, R.290, W.292 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.290, B:R.290

1 x AH2: 1-deoxy-alpha-D-mannopyranose(Non-functional Binders)

AH2.5: 1 residues within 4Å: Ligands: NAG.4 No protein-ligand interaction detected (PLIP)

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
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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ATP11C

Cell cycle control protein 50A

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