X-ray structure of IGLUR5 ligand-binding core (S1S2) in complex with dysiherbaine at 1.35A resolution

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 21% strand (DSSP).

Ligands and binding sites

• DYH · (2R,3aR,6S,7R,7aR)-2-[(2S)-2-amino-2-carboxyethyl]-6-hydroxy-7-(methylamino)hexahydro-2H-furo[3,2-b]pyran-2-carboxylic acid · ligand · 4 copies · chains A, B, C, D
• SO4 · Sulfate ion · ion · 2 copies · chains A, B
• CL · Chloride ion · ion · 2 copies · chains A, B
• GOL · Glycerol · additive · 3 copies · chains A, B, C

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

Pockets

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

Interfaces

5 interfaces between chains.

• A–C · 478 Ų buried · 5 hydrogen bonds · protein-protein
• B–D · 454 Ų buried · 5 hydrogen bonds · protein-protein
• B–C · 401 Ų buried · 4 hydrogen bonds · protein-protein
• A–B · 136 Ų buried · 0 hydrogen bonds · protein-protein
• C–D · 104 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

• 3GBA · X-ray structure of iGluR5 ligand-binding core (S1S2) in complex with dysiherbaine at… · the same entry in another collection · chain D against D, TM-score 1.00
• P22756 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 1 (P22756) · a predicted model of the same protein · chain C against A, TM-score 0.95

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 P22756
• Elsewhere: RCSB PDB 3GBA · PDBe 3GBA · UniProt P22756