Research workbench
Metabotropic glutamate receptor 5 extracellular domain in complex with NB43 and L-quisqualic acid
Analyse Metabotropic glutamate receptor 5 extracellular domain in complex with NB43 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N50
- Type
- protein
- Length
- 1,596 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metabotropic glutamate receptor 5; Nanobody 43
- UniProt
- P41594
- Ligands
- QUS, NAG
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metabotropic glutamate receptor 5 | protein | 518 | 32% helix, 22% strand | P41594 |
| B | Metabotropic glutamate receptor 5 | protein | 444 | 37% helix, 20% strand | P41594 |
| C | Metabotropic glutamate receptor 5 | protein | 511 | 34% helix, 19% strand | P41594 |
| E | Nanobody 43 | protein | 123 | 5% helix, 48% strand | — |
Ligands and binding sites
- QUS · (S)-2-amino-3-(3,5-dioxo-[1,2,4]oxadiazolidin-2-yl)-propionic acid · ligand · 3 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.78 | 0.80 | 84 | empty |
| 2 | 268 | 0.66 | 0.83 | 45 | QUS |
| 3 | 354 | 0.66 | 0.80 | 50 | QUS |
| 4 | 310 | 0.60 | 0.78 | 42 | empty |
| 5 | 218 | 0.56 | 0.78 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–C · 965 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 812 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 45 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6N50 · Metabotropic Glutamate Receptor 5 Extracellular Domain in Complex with Nb43 and… · the same entry in another collection · chain A against A, TM-score 1.00
- P41594 · AlphaFold monomer V2.0 prediction for metabotropic glutamate receptor 5 (P41594) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P41594
- Elsewhere: RCSB PDB 6N50 · PDBe 6N50 · UniProt P41594
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