Crystal structure of the kainate receptor GLUK3 ligand binding domain in complex with (S)-1-[2'-amino-2'-carboxyethyl]-6-methyl-5,7- DIHYDROPYRROLO[3,4-D]PYRIMIDIN-2,4(1H,3H)-dione at resolution 2.4A

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).

Ligands and binding sites

• CG8 · (2~{S})-2-azanyl-3-[6-methyl-2,4-bis(oxidanylidene)-5, 7-dihydropyrrolo[3,4-d]pyrimidin-1-yl]propanoic acid · ligand · 2 copies · chains A, B
• ZN · Zinc ion · metal · 5 copies · chains A, B
• CL · Chloride ion · ion · 3 copies · chains A, B
• SO4 · Sulfate ion · ion · chains B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 255 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

• 6F28 · Crystal structure of the kainate receptor GluK3 ligand binding domain in complex with… · the same entry in another collection · chain A against A, 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 6F28 · PDBe 6F28 · UniProt P42264