SMTL ID : 7whw.1

Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in detergent with AMPPCP (E1-ATP state)

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: 14 residues within 4Å: Chain A: Y.585 Chain B: F.152, K.154, N.236, S.237, M.238, N.240, P.287, Y.288, E.290, K.291, H.347, W.348, P.349 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.290 Hydrophobic interactions: B:Y.288, B:P.349

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

ACP.2: 19 residues within 4Å: Chain A: D.667, T.669, S.798, D.800, E.801, F.842, S.844, K.847, M.849, K.871, R.909, T.910, L.911, T.989, G.990, K.992, V.1105, N.1133 Ligands: MG.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.668, A:T.669, A:S.798, A:S.798, A:S.844, A:R.909, A:T.989, A:T.989, A:G.990, A:K.992, A:N.1133 pi-Stacking: A:F.842, A:F.842

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.667, G.670, D.1130, N.1133 Ligands: ACP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.667

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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