Cryo-EM structure of DRS2P-CDC50P in the E1-alfx-ADP state

Structure

electron microscopy · 2 distinct chains · 40% helix, 18% strand (DSSP).

Ligands and binding sites

• ALF · Tetrafluoroaluminate ion · ligand · chains A
• ADP · Adenosine-5'-diphosphate · ligand · chains A
• 2Y5 · (2R)-1-{[(R)-hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-tetrahydroxy-4-(phosphonooxy) cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy) propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate · ligand · chains A, C
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains C
• BMA · beta-D-mannopyranose · sugar · 2 copies
• MG · Magnesium ion · metal · 2 copies · chains A

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–C · 4762 Ų buried · 34 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

• 7OH5 · Cryo-EM structure of Drs2p-Cdc50p in the E1-AlFx-ADP state · the same entry in another collection · chain A against A, TM-score 1.00
• P39524 · AlphaFold monomer V2.0 prediction for probable phospholipid- transporting ATPase DRS2… · a predicted model of the same protein · chain A against A, TM-score 0.76

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 P39524
• Every structure of UniProt A0A6L0Z5H3
• Elsewhere: RCSB PDB 7OH5 · PDBe 7OH5 · UniProt P39524 · UniProt A0A6L0Z5H3