SMTL ID : 7dsi.1

Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in yeast lipids with AMPPCP ( resting state )

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain B: Y.293, D.295, N.298, E.299, N.301 No protein-ligand interaction detected (PLIP)

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.2: 14 residues within 4Å: Chain B: F.152, K.154, N.236, M.238, F.239, N.240, P.287, Y.288, W.289, E.290, K.291, H.347, W.348, P.349 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.349 Hydrogen bonds: B:E.290, B:E.290

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 4 residues within 4Å: Chain B: Q.246, T.248, S.254, N.256 No protein-ligand interaction detected (PLIP)

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.4: 23 residues within 4Å: Chain A: D.667, K.668, T.669, S.798, D.800, E.801, F.842, S.844, K.847, M.849, K.871, G.872, A.873, R.909, T.910, L.911, T.989, G.990, D.991, R.1104, K.1110, N.1133 Ligands: MG.5 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:D.667, A:D.667, A:K.668, A:T.669, A:S.798, A:D.800, A:E.801, A:E.801, A:R.909, A:T.910, A:T.989, A:G.990, A:G.990, A:R.1104, A:R.1104, A:K.1110, A:N.1133 pi-Stacking: A:F.842, A:F.842

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: D.667, T.669, D.1130 Ligands: ACP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.667, A:T.669

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, J. et al., Conformational changes of a phosphatidylcholine flippase in lipid membranes. Cell Rep (2022)

Release Date

2022-03-23

Peptides

Phospholipid-transporting ATPase DNF1: A
Alkylphosphocholine resistance protein LEM3: 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 DNF1

Alkylphosphocholine resistance protein LEM3

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