GLUN1B-GLUN2B NMDA receptor in complex with sdz 220-040 and L689,560, class 1

Structure

electron microscopy · 2 distinct chains · 36% helix, 13% strand (DSSP).

Ligands and binding sites

• QGM · (2R,4S)-5,7-dichloro-4-[(phenylcarbamoyl)amino]-1,2,3,4-tetrahydroquinoline-2-carboxylic acid · ligand · 2 copies · chains A, C
• QGP · (2S)-2-amino-3-[2',4'-dichloro-4-hydroxy-5-(phosphonomethyl)biphenyl-3-yl]propanoic acid · ligand · 2 copies · chains B, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains B, D, A, 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, 20 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 3342 Ų buried · 8 hydrogen bonds · protein-protein
• C–D · 3319 Ų buried · 8 hydrogen bonds · protein-protein
• A–D · 3068 Ų buried · 11 hydrogen bonds · protein-protein
• B–C · 3024 Ų buried · 9 hydrogen bonds · protein-protein
• B–D · 246 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 18 disulfide, 10 glycan (disulfide, N-glycosylation).

Compared structures

• 6WHU · GluN1b-GluN2B NMDA receptor in complex with SDZ 220-040 and L689,560, class 1 · the same entry in another collection · chain D against D, 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 C against A, TM-score 0.91
• Q00960 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2B (Q00960) · a predicted model of the same protein · chain B against A, TM-score 0.89

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 Q00960
• Elsewhere: RCSB PDB 6WHU · PDBe 6WHU · UniProt P35439 · UniProt Q00960