Research workbench
GLUN1B-GLUN2B NMDA receptor in complex with GLUN1 antagonist L689,560, class 1
Analyse GLUN1B-GLUN2B NMDA receptor in complex with GLUN1 antagonist L689,560, class 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WHY
- Type
- protein
- Length
- 3,098 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ionotropic glutamate receptor , NMDA receptor GLUN1B; Ionotropic glutamate receptor…
- Ligands
- QGM, NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ionotropic glutamate receptor , NMDA receptor GLUN1B | protein | 790 | 36% helix, 17% strand | — |
| B, D | Ionotropic glutamate receptor , NMDA receptor GLUN2B | protein | 759 | 36% helix, 14% strand | — |
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
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, D
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.83 | 0.87 | 103 | empty |
| 2 | 1129 | 0.83 | 0.84 | 165 | empty |
| 3 | 1113 | 0.82 | 0.83 | 143 | empty |
| 4 | 929 | 0.82 | 0.83 | 128 | empty |
| 5 | 949 | 0.82 | 0.83 | 118 | empty |
Interfaces
5 interfaces between chains.
- A–D · 2895 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 2841 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2759 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 2718 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 133 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 6WHY · GluN1b-GluN2B NMDA receptor in complex with GluN1 antagonist L689,560, class 1 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6WHY · PDBe 6WHY
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