Crystal structure of the GLUK1 ligand-binding domain in complex with kainate and bpam-121 at 2.10 a resolution

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).

Ligands and binding sites

• 7M6 · 7-chloro-4-(2-fluoroethyl)-2,3-dihydro-1,2,4-benzothiadiazine 1,1-dioxide · ligand · 2 copies · chains A, B
• KAI · 3-(carboxymethyl)-4-isopropenylproline · ligand · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 5 copies · chains A, B
• CL · Chloride ion · ion · chains A, B
• GOL · Glycerol · additive · 2 copies · chains A, B
• ACT · Acetate ion · additive · chains A

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1089 Ų buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

• 5MFW · Crystal structure of the GluK1 ligand-binding domain in complex with kainate and BPAM-121… · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.98

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 5MFW · PDBe 5MFW · UniProt P22756