Research workbench
GLUN1B-GLUN2B NMDA receptor in complex with GLUN2B antagonist sdz 220- 040, class 2
Analyse GLUN1B-GLUN2B NMDA receptor in complex with GLUN2B antagonist sdz 220- 040… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WHX
- Type
- protein
- Length
- 3,154 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
- QGP, NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 32% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ionotropic glutamate receptor , NMDA receptor GLUN1B | protein | 791 | 34% helix, 11% strand | — |
| B, D | Ionotropic glutamate receptor , NMDA receptor GLUN2B | protein | 784 | 32% helix, 13% strand | — |
| C | Ionotropic glutamate receptor , NMDA receptor GLUN1B | protein | 795 | 30% helix, 9% strand | — |
Ligands and binding sites
- QGP · (2S)-2-amino-3-[2',4'-dichloro-4-hydroxy-5-(phosphonomethyl)biphenyl-3-yl]propanoic acid · ligand · 2 copies · chains B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains 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 | 773 | 0.85 | 0.88 | 73 | empty |
| 2 | 833 | 0.83 | 0.86 | 117 | empty |
| 3 | 521 | 0.80 | 0.86 | 83 | empty |
| 4 | 866 | 0.80 | 0.82 | 91 | empty |
| 5 | 1114 | 0.79 | 0.81 | 103 | empty |
Interfaces
6 interfaces between chains.
- B–C · 3486 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 3452 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 3431 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 3370 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 395 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 covalent, 2 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 6WHX · GluN1b-GluN2B NMDA receptor in complex with GluN2B antagonist SDZ 220-040, class 2 · 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 6WHX · PDBe 6WHX
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