SMTL ID : 7f7f.1

Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in yeast lipids with beryllium fluoride (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: 6 residues within 4Å: Chain B: Y.293, D.295, N.298, E.299, T.300, 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: 13 residues within 4Å: Chain A: Y.585 Chain B: T.153, N.236, S.237, M.238, F.239, N.240, Y.288, W.289, K.291, H.347, W.348, P.349 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.288, B:P.349, A:Y.585

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: 2 residues within 4Å: Chain B: Q.246, N.256 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: D.667, T.669, D.1130 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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