Human ATP13A2 in the outward-facing E2 state bound to spermine and magnesium fluoride

Structure

electron microscopy · 1 distinct chain · 44% helix, 18% strand (DSSP).

Ligands and binding sites

• D10 · Decane · ligand · 9 copies · chains A
• CLR · Cholesterol · ligand · 4 copies · chains A
• Y01 · Cholesterol hemisuccinate · ligand · 3 copies · chains A
• MF4 · Tetrafluoromagnesate(2-) · ligand · chains A
• C14 · Tetradecane · ligand · chains A
• D12 · Dodecane · ligand · chains A
• SPK · Spermine (fully protonated form) · ligand · chains A
• EUJ · (2R)-3-{[(S)-hydroxy{[(1s,2r,3r,4s,5s,6r)-2,4,6-trihydroxy-3,5-bis(phosphonooxy) cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
• MG · Magnesium ion · metal · chains A
• LMT · Dodecyl-beta-D-maltoside · additive · chains A

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

Pockets

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

Modifications

Observed in the structure: 1 glycan (N-glycosylation).

Compared structures

• 7M5Y · human ATP13A2 in the outward-facing E2 state bound to spermine and magnesium fluoride · the same entry in another collection · chain A against A, TM-score 1.00
• Q9NQ11 · AlphaFold monomer V2.0 prediction for polyamine-transporting ATPase 13A2 (Q9NQ11) · a predicted model of the same protein · chain A against A, TM-score 0.84

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 Q9NQ11
• Elsewhere: RCSB PDB 7M5Y · PDBe 7M5Y · UniProt Q9NQ11