Research workbench
Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-108
Analyse Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8G18
- Type
- protein
- Length
- 1,443 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.85
- Source
- Rattus norvegicus; Xenopus laevis
- Molecule
- Glutamate receptor ionotropic, NMDA 1; Glutamate receptor ionotropic, NMDA 2B
- UniProt
- A0A1L8F5J9, Q00960
- Ligands
- YGW, NAG, MAN, BMA, NA
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.85 · 3 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 359 | 36% helix, 24% strand | A0A1L8F5J9 |
| B, D | Glutamate receptor ionotropic, NMDA 2B | protein | 363 | 31% helix, 21% strand | Q00960 |
| C | Glutamate receptor ionotropic, NMDA 1 | protein | 358 | 36% helix, 23% strand | A0A1L8F5J9 |
Ligands and binding sites
- YGW · N-(4-{3-[4-(3,4-difluorophenyl)piperazin-1-yl]-2-oxopropoxy}phenyl)methanesulfonamide · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 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
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.78 | 0.81 | 90 | YGW |
| 2 | 1035 | 0.78 | 0.80 | 107 | YGW |
| 3 | 187 | 0.70 | 0.87 | 41 | empty |
| 4 | 122 | 0.61 | 0.86 | 34 | empty |
| 5 | 98 | 0.57 | 0.86 | 32 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1266 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1230 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 697 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 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 0.96
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 A0A1L8F5J9
- Every structure of UniProt Q00960
- Elsewhere: RCSB PDB 8G18 · PDBe 8G18 · UniProt A0A1L8F5J9 · UniProt Q00960
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.