Crystal structure of the orexin-1 receptor in complex with empa

Structure

x-ray diffraction · 2 distinct chains · 80% helix, 3% strand (DSSP).

Ligands and binding sites

• SOG · octyl 1-thio-beta-D-glucopyranoside · ligand · 47 copies · chains A, B
• 7MA · N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl) sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide · ligand · 2 copies · chains A, B
• PGW · (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate · ligand · 2 copies · chains A, B
• NA · Sodium ion · metal · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 3 copies · chains A, B
• PG4 · Tetraethylene glycol · additive · 5 copies · chains A, B
• CIT · Citric acid · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 985 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

• 6TOD · Crystal structure of the Orexin-1 receptor in complex with EMPA · the same entry in another collection · chain A against A, TM-score 1.00
• O43613 · AlphaFold monomer V2.0 prediction for orexin receptor type 1 (O43613) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 O43613
• Elsewhere: RCSB PDB 6TOD · PDBe 6TOD · UniProt O43613