Xfel crystal structure of the human sphingosine 1 phosphate receptor 5 in complex with ono-5430608

Structure

x-ray diffraction · 2 distinct chains · 80% helix, 1% strand (DSSP).

Ligands and binding sites

• B2O · 4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid · ligand · 2 copies · chains A, B
• OLA · Oleic acid · ligand · 2 copies · chains B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
• OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 3 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 458 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 7YXA · XFEL crystal structure of the human sphingosine 1 phosphate receptor 5 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9H228 · AlphaFold monomer V2.0 prediction for sphingosine 1-phosphate receptor 5 (Q9H228) · a predicted model of the same protein · chain A against A, TM-score 0.77
• P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain B against A, TM-score 0.26

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 Q9H228
• Every structure of UniProt P0ABE7
• Elsewhere: RCSB PDB 7YXA · PDBe 7YXA · UniProt Q9H228 · UniProt P0ABE7