Structure of the GLUA2 ligand-binding domain (L483Y-N754S) in complex with glutamate and BPAM549

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
• QSZ · (4~{S})-4-cyclopropyl-7-fluoranyl-3,4-dihydro-2~{H}-thiochromene 1,1-dioxide · ligand · 3 copies · chains A, B, C
• QSW · (4~{R})-4-cyclopropyl-7-fluoranyl-3,4-dihydro-2~{H}-thiochromene 1,1-dioxide · ligand · 3 copies · chains A, B, C
• ZN · Zinc ion · metal · 8 copies · chains A, B, C
• CL · Chloride ion · ion · 5 copies · chains A, B, C
• GOL · Glycerol · additive · 6 copies · chains A, C, B
• ACT · Acetate ion · additive · 5 copies · chains A, B, C
• CAC · Cacodylate ion · additive · chains A, B

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

Pockets

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

Interfaces

3 interfaces between chains.

• B–C · 1004 Ų buried · 10 hydrogen bonds · protein-protein
• A–B · 348 Ų buried · 9 hydrogen bonds · protein-protein
• A–C · 83 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 covalent (disulfide, additive adduct).

Compared structures

• 6ZYU · Structure of the GluA2 ligand-binding domain (L483Y-N754S) in complex with glutamate and… · the same entry in another collection · chain B against B, TM-score 1.00
• P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · 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 P19491
• Elsewhere: RCSB PDB 6ZYU · PDBe 6ZYU · UniProt P19491