Structure of GLUA2CRYST in complex the antagonist ZK200775 and the negative allosteric modulator GYKI53655 at 4.65 a resolution

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 18% strand (DSSP).

Ligands and binding sites

• GYK · (8R)-5-(4-aminophenyl)-N,8-dimethyl-8,9-dihydro-2H,7H-[1,3]dioxolo[4,5-h][2,3]benzodiazepine-7-carboxamide · ligand · 4 copies · chains A, B, D, C
• ZK1 · {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid · ligand · 4 copies · chains A, B, C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
• BMA · beta-D-mannopyranose · sugar · 4 copies · chains B

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 4038 Ų buried · 35 hydrogen bonds · protein-protein
• C–D · 3715 Ų buried · 37 hydrogen bonds · protein-protein
• A–C · 3321 Ų buried · 14 hydrogen bonds · protein-protein
• B–D · 3299 Ų buried · 17 hydrogen bonds · protein-protein
• B–C · 432 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

• 6RUQ · Structure of GluA2cryst in complex the antagonist ZK200775 and the negative allosteric… · the same entry in another collection · chain D against D, TM-score 1.00
• P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain A against A, TM-score 0.85

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 P19491
• Elsewhere: RCSB PDB 6RUQ · PDBe 6RUQ · UniProt P19491