MolNFT v1 · #147268 · protein
Heterodimer of the GLUN1B-GLUN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-4
6E7R · Glutamate receptor ionotropic, NMDA 1: “Heterodimer of the GLUN1B-GLUN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-4”. X-ray diffraction, 6 ligands (HYS, NAG, MAN), 16 pockets (best druggability 0.78).…
- PDB
- 6E7R
- Type
- protein
- Length
- 1,436 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
- HYS, NAG, MAN, BMA, NA, CL
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 358 | 37% helix, 25% strand | A0A1L8F5J9 |
| B | Glutamate receptor ionotropic, NMDA 2B | protein | 363 | 34% helix, 23% strand | Q00960 |
| C | Glutamate receptor ionotropic, NMDA 1 | protein | 357 | 37% helix, 25% strand | A0A1L8F5J9 |
| D | Glutamate receptor ionotropic, NMDA 2B | protein | 358 | 32% helix, 23% strand | Q00960 |
Ligands and binding sites
- HYS · N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, C, B, 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 · 12 copies · chains A, B, C, D
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 | 892 | 0.78 | 0.81 | 89 | HYS, CL |
| 2 | 871 | 0.78 | 0.81 | 89 | HYS, CL |
| 3 | 251 | 0.71 | 0.86 | 43 | empty |
| 4 | 122 | 0.64 | 0.88 | 32 | CL |
| 5 | 94 | 0.62 | 0.89 | 31 | CL |
Interfaces
3 interfaces between chains.
- A–B · 1272 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1235 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 669 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 6E7R · 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 6E7R · PDBe 6E7R · UniProt A0A1L8F5J9 · UniProt Q00960
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