Research workbench
Heterodimer of the GLUN1B-GLUN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-6
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
- 6E7T
- Type
- protein
- Length
- 1,420 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 1; Glutamate receptor ionotropic, NMDA 2B
- UniProt
- A0A1L8F5J9, Q00960
- Ligands
- HYY, NAG, MAN, BMA, NA, CL
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor ionotropic, NMDA 1 | protein | 355 | 37% helix, 25% strand | A0A1L8F5J9 |
| B | Glutamate receptor ionotropic, NMDA 2B | protein | 356 | 33% helix, 23% strand | Q00960 |
| D | Glutamate receptor ionotropic, NMDA 2B | protein | 354 | 32% helix, 23% strand | Q00960 |
Ligands and binding sites
- HYY · N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propyl) amino}-2-hydroxypropoxy]phenyl}methanesulfonamide · 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
- CL · Chloride ion · ion · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.77 | 0.81 | 89 | CL, HYY |
| 2 | 762 | 0.76 | 0.80 | 83 | CL, HYY |
| 3 | 273 | 0.75 | 0.88 | 48 | empty |
| 4 | 83 | 0.63 | 0.91 | 24 | CL |
| 5 | 107 | 0.61 | 0.87 | 31 | CL |
Interfaces
3 interfaces between chains.
- C–D · 1217 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1214 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 708 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 6E7T · Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.96
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 6E7T · PDBe 6E7T · UniProt A0A1L8F5J9 · UniProt Q00960
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