Research workbench
GLUN1B-GLUN2B NMDA receptor in active conformation stabilized by inter-GLUN1B-GLUN2B subunit cross-linking
Analyse GLUN1B-GLUN2B NMDA receptor in active conformation stabilized by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WI1
- Type
- protein
- Length
- 3,182 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
- NAG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 2 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ionotropic glutamate receptor , NMDA receptor GLUN1B | protein | 806 | 38% helix, 16% strand | — |
| B, D | Ionotropic glutamate receptor , NMDA receptor GLUN2B | protein | 785 | 37% helix, 14% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1055 | 0.89 | 0.90 | 153 | empty |
| 2 | 931 | 0.81 | 0.83 | 122 | empty |
| 3 | 920 | 0.80 | 0.82 | 82 | empty |
| 4 | 1197 | 0.79 | 0.80 | 90 | empty |
| 5 | 1114 | 0.78 | 0.80 | 121 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3152 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 3134 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 2597 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 2556 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 285 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6WI1 · GluN1b-GluN2B NMDA receptor in active conformation stabilized by inter-GluN1b-GluN2B… · 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 6WI1 · PDBe 6WI1
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