Structure of GLUK3 ligand-binding domain (S1S2) in complex with the agonist lm-12B at 2.10 a resolution

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).

Ligands and binding sites

• 8VE · (3~{a}~{R},4~{S},6~{a}~{R})-1-methyl-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-c]pyrazole-3,4-dicarboxylic acid · ligand · 2 copies · chains B, A
• ZN · Zinc ion · metal · 6 copies · chains B, A
• CL · Chloride ion · ion · 5 copies · chains B, A
• GOL · Glycerol · additive · 5 copies · chains B, A
• ACT · Acetate ion · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• B–A · 253 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

• 5O4F · Structure of GluK3 ligand-binding domain (S1S2) in complex with the agonist LM-12b at… · the same entry in another collection · chain B against B, TM-score 1.00
• P42264 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 3 (P42264) · a predicted model of the same protein · chain B 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 P42264
• Elsewhere: RCSB PDB 5O4F · PDBe 5O4F · UniProt P42264