Crystal structure of GLUN1/GLUN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-(3-FLUOROPROPYL)PHENYL-acepc

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).

Ligands and binding sites

• GLY · Glycine · ligand · chains A
• 5DY · 5-[(2R)-2-amino-2-carboxyethyl]-1-[4-(3-fluoropropyl) phenyl]-1H-pyrazole-3-carboxylic acid · ligand · chains A, B
• PEG · Di(hydroxyethyl)ether · additive · chains A, B
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1287 Ų buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 covalent (disulfide, additive adduct).

Compared structures

• 5VII · Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and… · the same entry in another collection · chain B against B, TM-score 1.00
• 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
• 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 0.95

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
• Every structure of UniProt G3V9C5
• Elsewhere: RCSB PDB 5VII · PDBe 5VII · UniProt P35439 · UniProt Q00959 · UniProt G3V9C5