Cryo-EM structure of the partially activated DRS2P-CDC50P

Structure

electron microscopy · 2 distinct chains · 32% helix, 16% strand (DSSP).

Ligands and binding sites

• 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
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains C
• BMA · beta-D-mannopyranose · sugar · 2 copies · chains C
• MG · Magnesium ion · metal · chains A

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

Pockets

18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–C · 4214 Ų buried · 32 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 glycan, 2 disulfide, 1 covalent, 1 modified (N-glycosylation, disulfide, covalent ligand, nonstandard).

Compared structures

• 6ROI · Cryo-EM structure of the partially activated Drs2p-Cdc50p · 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 0.99
• P25656 · AlphaFold monomer V2.0 prediction for cell division control protein 50 (P25656) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 P25656
• Elsewhere: RCSB PDB 6ROI · PDBe 6ROI · UniProt P39524 · UniProt P25656