Structure of GLUK1 ligand-binding domain (S1S2) in complex with (S)-2- amino-4-(2,3-dioxo-1,2,3,4-tetrahydroquinoxalin-6-YL)BUTANOIC acid at 2.28 a resolution

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 24% strand (DSSP).

Ligands and binding sites

• 35K · (2S)-2-amino-4-(2,3-dioxo-1,2,3,4-tetrahydroquinoxalin-6-yl)butanoic acid · ligand · 3 copies · chains A, B, C
• SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
• CL · Chloride ion · ion · chains A
• GOL · Glycerol · additive · 3 copies · chains B
• PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
• ACT · Acetate ion · additive · chains A, C

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

Pockets

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

Interfaces

3 interfaces between chains.

• A–C · 1131 Ų buried · 9 hydrogen bonds · protein-protein
• B–C · 485 Ų buried · 2 hydrogen bonds · protein-protein
• A–B · 65 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 4QF9 · Structure of GluK1 ligand-binding domain (S1S2) in complex with… · 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 0.90

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 4QF9 · PDBe 4QF9 · UniProt P22756