Structure of the S. cerevisiae phosphatidylcholine flippase DNF1-LEM3 complex in the E1-ADP state

Structure

electron microscopy · 2 distinct chains · 46% helix, 14% strand (DSSP).

Ligands and binding sites

• POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · chains A, B
• ADP · Adenosine-5'-diphosphate · ligand · chains A
• ALF · Tetrafluoroaluminate ion · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
• MAN · alpha-D-mannopyranose · sugar
• MG · Magnesium ion · metal · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 4927 Ų buried · 45 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

• 7KYB · Structure of the S. cerevisiae phosphatidylcholine flippase Dnf1-Lem3 complex in the… · the same entry in another collection · chain A against A, TM-score 1.00
• P42838 · AlphaFold monomer V2.0 prediction for alkylphosphocholine resistance protein LEM3 (P42838) · a predicted model of the same protein · chain B against A, TM-score 0.98
• P32660 · AlphaFold monomer V2.0 prediction for phospholipid-transporting ATPase DNF1 (P32660) · a predicted model of the same protein · chain A against A, TM-score 0.80

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P32660
• Every structure of UniProt P42838
• Elsewhere: RCSB PDB 7KYB · PDBe 7KYB · UniProt P32660 · UniProt P42838