Human sigma-1 receptor bound to (+)-pentazocine

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 29% strand (DSSP).

Ligands and binding sites

• GM4 · (2S,6S,11S)-6,11-dimethyl-3-(3-methylbut-2-en-1-yl)-1, 2,3,4,5,6-hexahydro-2,6-methano-3-benzazocin-8-ol · ligand · 3 copies · chains A, B, C
• SO4 · Sulfate ion · ion · 14 copies · chains A, B, C
• OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 11 copies · chains A, B, C
• GOL · Glycerol · additive · 4 copies · chains A, B, C

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 1022 Ų buried · 16 hydrogen bonds · protein-protein
• B–C · 1016 Ų buried · 9 hydrogen bonds · protein-protein
• A–C · 1012 Ų buried · 13 hydrogen bonds · protein-protein

Compared structures

• 6DK1 · Human sigma-1 receptor bound to (+)-pentazocine · the same entry in another collection · chain A against A, TM-score 1.00
• Q99720 · AlphaFold monomer V2.0 prediction for sigma non-opioid intracellular receptor 1 (Q99720) · a predicted model of the same protein · chain A against A, TM-score 0.89

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 Q99720
• Elsewhere: RCSB PDB 6DK1 · PDBe 6DK1 · UniProt Q99720