Crystal structures of GLUR2 ligand-binding-domain in complex with glutamate and positive allosteric modulators

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).

Ligands and binding sites

• GLU · Glutamic acid · ligand · 3 copies · chains A, B, C
• 1YX · N-[(3S)-1-{2-fluoro-4-[(5S)-5-{[(propan-2-ylsulfonyl)amino]methyl}-4,5-dihydro-1,2-oxazol-3-yl]phenyl}pyrrolidin-3-yl]acetamide · ligand · 2 copies · chains A, C, B
• ZN · Zinc ion · metal · 5 copies · chains A, B, C

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

Pockets

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

Interfaces

3 interfaces between chains.

• A–C · 910 Ų buried · 11 hydrogen bonds · protein-protein
• A–B · 294 Ų buried · 7 hydrogen bonds · protein-protein
• B–C · 78 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

• 4LZ8 · Crystal structures of GLuR2 ligand-binding-domain in complex with glutamate and positive… · the same entry in another collection · chain A against A, 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 0.98

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 P19491
• Elsewhere: RCSB PDB 4LZ8 · PDBe 4LZ8 · UniProt P19491