Structure of the ligand-binding and transmembrane domains of kainate receptor GluK2 in complex with the positive allosteric modulator BPAM344 and noncompetitive inhibitor perampanel

Structure

electron microscopy · resolution 3.1 · 1 distinct chain · 45% helix, 11% strand (DSSP).

Ligands and binding sites

• POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 16 copies · chains A, D, B, C
• 2J9 · 4-cyclopropyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide · ligand · 4 copies · chains A, D, B, C
• 6ZP · 2-(6'-oxo-1'-phenyl[1',6'-dihydro[2,3'-bipyridine]]-5'-yl)benzonitrile · ligand · 2 copies · chains A, B, D, C
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, C, D
• BMA · beta-D-mannopyranose · sugar · 4 copies · chains B, D
• NA · Sodium ion · metal · 7 copies · chains A, B, C, D
• CL · Chloride ion · ion · 2 copies · chains A, D, B, C

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–D · 3589 Ų buried · 35 hydrogen bonds · protein-protein
• B–C · 3573 Ų buried · 36 hydrogen bonds · protein-protein
• A–B · 2375 Ų buried · 18 hydrogen bonds · protein-protein
• C–D · 2288 Ų buried · 17 hydrogen bonds · protein-protein
• A–C · 135 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 glycan, 6 disulfide (N-glycosylation, disulfide).

Compared structures

• P42260 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 2 (P42260) · a predicted model of the same protein · chain D against A, TM-score 0.72

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 P42260
• Elsewhere: RCSB PDB 8FWW · PDBe 8FWW · UniProt P42260