Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1 and GLUN2B in complex with ifenprodil

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 24% strand (DSSP).

Ligands and binding sites

• QEL · 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol · ligand · 2 copies · chains A, B, C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
• MAN · alpha-D-mannopyranose · sugar · 2 copies
• BMA · beta-D-mannopyranose · sugar
• NA · Sodium ion · metal · 2 copies · chains A, C

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

Pockets

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

Interfaces

3 interfaces between chains.

• C–D · 1263 Ų buried · 17 hydrogen bonds · protein-protein
• A–B · 1247 Ų buried · 13 hydrogen bonds · protein-protein
• B–D · 775 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 glycan, 4 disulfide (N-glycosylation, disulfide).

Compared structures

• 5EWJ · Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1 and GLUN2B… · the same entry in another collection · chain A against A, TM-score 1.00
• Q13224 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2B (Q13224) · a predicted model of the same protein · chain B 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 Q91977
• Every structure of UniProt Q13224
• Elsewhere: RCSB PDB 5EWJ · PDBe 5EWJ · UniProt Q91977 · UniProt Q13224