S-(+)-ketamine bound GLUN1A-GLUN2B NMDA receptors at 3.69 ångström resolution

Structure

electron microscopy · 2 distinct chains · 37% helix, 16% strand (DSSP).

Ligands and binding sites

• GLY · Glycine · ligand · 2 copies · chains A, C
• GLU · Glutamic acid · ligand · 2 copies · chains B, D
• JC9 · (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one · ligand · chains A, B, C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains B, C, D, A

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

5 interfaces between chains.

• A–B · 3011 Ų buried · 10 hydrogen bonds · protein-protein
• C–D · 2988 Ų buried · 7 hydrogen bonds · protein-protein
• B–C · 2806 Ų buried · 9 hydrogen bonds · protein-protein
• A–D · 2768 Ų buried · 6 hydrogen bonds · protein-protein
• B–D · 118 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

• 7SAC · S-(+)-ketamine bound GluN1a-GluN2B NMDA receptors at 3.69 Angstrom resolution · 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 0.93
• Q00960 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2B (Q00960) · a predicted model of the same protein · chain D against A, TM-score 0.92

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 7SAC · PDBe 7SAC · UniProt P35439 · UniProt Q00960