Glutamate- and glycine-bound GLUN1/GLUN2A agonist binding domains with mpx 007

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).

Ligands and binding sites

• GLY · Glycine · ligand · chains A
• GLU · Glutamic acid · ligand · chains B
• 67Q · 5-({[(3,4-difluorophenyl)sulfonyl]amino}methyl)-6-methyl-N-[(2-methyl-4H-1lambda~4~,3-thiazol-5-yl)methyl]pyrazine-2-carboxamide · ligand · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1213 Ų buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

• 5I59 · Glutamate- and glycine-bound GluN1/GluN2A agonist binding domains with MPX 007 · the same entry in another collection · chain B against B, TM-score 1.00
• Q00959 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (Q00959) · a predicted model of the same protein · chain B against A, TM-score 0.98
• P35439 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (P35439) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P35439
• Every structure of UniProt Q00959
• Elsewhere: RCSB PDB 5I59 · PDBe 5I59 · UniProt P35439 · UniProt Q00959