MolNFT v1 · #157609 · protein
Metabotropic glutamate receptor 5 extracellular domain with NB43
6N4Y: “Metabotropic glutamate receptor 5 extracellular domain with NB43”. X-ray diffraction, 4 ligands (NAG, FUC, MAN), 20 pockets (best druggability 0.69). MolNFT v1 #157609 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6N4Y
- Type
- protein
- Length
- 2,503 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metabotropic glutamate receptor 5; Nanobody 43
- UniProt
- P41594
- Ligands
- NAG, FUC, MAN, BMA
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metabotropic glutamate receptor 5 | protein | 507 | 34% helix, 19% strand | P41594 |
| B | Metabotropic glutamate receptor 5 | protein | 517 | 32% helix, 21% strand | P41594 |
| C | Metabotropic glutamate receptor 5 | protein | 480 | 35% helix, 21% strand | P41594 |
| D | Metabotropic glutamate receptor 5 | protein | 511 | 33% helix, 21% strand | P41594 |
| E, F, G | Nanobody 43 | protein | 123 | 5% helix, 50% strand | — |
| H | Nanobody 43 | protein | 119 | 8% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains C, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.69 | 0.76 | 51 | empty |
| 2 | 871 | 0.68 | 0.74 | 67 | empty |
| 3 | 397 | 0.58 | 0.75 | 46 | empty |
| 4 | 310 | 0.58 | 0.77 | 28 | empty |
| 5 | 364 | 0.57 | 0.76 | 40 | empty |
Interfaces
9 interfaces between chains.
- B–D · 1099 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 798 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 794 Ų buried · 13 hydrogen bonds · protein-protein
- D–G · 776 Ų buried · 11 hydrogen bonds · protein-protein
- C–H · 661 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6N4Y · Metabotropic Glutamate Receptor 5 Extracellular Domain with Nb43 · the same entry in another collection · chain H against H, TM-score 1.00
- P41594 · AlphaFold monomer V2.0 prediction for metabotropic glutamate receptor 5 (P41594) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 6N4Y · PDBe 6N4Y · UniProt P41594
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.