SMTL ID : 7dsh.1

Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in 90PS with AMPPCP (E1-ATP state)

Coordinates

PDB Format

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: 13 residues within 4Å: Chain A: Y.585 Chain B: F.152, N.236, S.237, M.238, N.240, P.287, Y.288, E.290, K.291, H.347, W.348, P.349 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.290 Hydrophobic interactions: B:P.349

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Covalent)

ACP.2: 17 residues within 4Å: Chain A: K.668, T.669, D.800, E.801, F.842, S.844, K.847, M.849, K.871, R.909, T.910, L.911, T.989, G.990, D.991, K.992 Ligands: MG.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.800, A:E.801, A:T.989, A:T.989, A:K.992, A:K.992, A:N.1133

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: K.668, G.670, D.1130, D.1134 Ligands: ACP.2 No protein-ligand interaction detected (PLIP)

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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