MolNFT v1 · #168483 · protein
GLUN1B-GLUN2B NMDA receptor in complex with GLUN1 antagonist L689,560, class 2
6WI0 · Glutamate receptor ionotropic, NMDA 1: “GLUN1B-GLUN2B NMDA receptor in complex with GLUN1 antagonist L689,560, class 2”. Electron microscopy, 2 ligands (QGM, NAG), 20 pockets (best druggability 0.87). MolNFT v1 #168483 on GenesisL1…
- PDB
- 6WI0
- Type
- protein
- Length
- 3,112 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 1; Glutamate receptor ionotropic, NMDA 2B
- UniProt
- P35439, Q00960
- Ligands
- QGM, NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor ionotropic, NMDA 1 | protein | 792 | 36% helix, 15% strand | P35439 |
| B, D | Glutamate receptor ionotropic, NMDA 2B | protein | 764 | 36% helix, 15% strand | Q00960 |
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 · 8 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 | 915 | 0.87 | 0.88 | 131 | empty |
| 2 | 822 | 0.82 | 0.85 | 95 | QGM |
| 3 | 1124 | 0.82 | 0.83 | 130 | empty |
| 4 | 945 | 0.81 | 0.83 | 109 | empty |
| 5 | 783 | 0.81 | 0.84 | 114 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2619 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 2580 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 2309 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 2306 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 6WI0 · GluN1b-GluN2B NMDA receptor in complex with GluN1 antagonist L689,560, class 2 · the same entry in another collection · chain D against D, TM-score 1.00
- P35439 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (P35439) · a predicted model of the same protein · chain A against A, TM-score 0.95
- 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 0.93
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 P35439
- Every structure of UniProt Q00960
- Elsewhere: RCSB PDB 6WI0 · PDBe 6WI0 · UniProt P35439 · UniProt Q00960
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.