Cryo-EM structure of DNF1 from saccharomyces cerevisiae in detergent with beryllium fluoride (E2P state)

Structure

electron microscopy · 2 distinct chains · 38% helix, 17% strand (DSSP).

Ligands and binding sites

• 6PL · (4S,7R)-4-hydroxy-N,N,N-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide · ligand · 2 copies · chains A, B
• BEF · Beryllium trifluoride ion · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
• BMA · beta-D-mannopyranose · sugar
• MG · Magnesium ion · metal · chains A

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

Pockets

19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 4864 Ų buried · 64 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 1 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).

Compared structures

• 7WHV · Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in detergent with beryllium… · the same entry in another collection · chain A against A, TM-score 1.00
• 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 0.98
• 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

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 7WHV · PDBe 7WHV · UniProt P32660 · UniProt P42838