MolNFT v1 · #157612 · protein
Metabotropic glutamate receptor 5 bound to L-quisqualate and NB43
6N51: “Metabotropic glutamate receptor 5 bound to L-quisqualate and NB43”. Electron microscopy, 2 ligands (QUS, NAG), 20 pockets (best druggability 0.86). MolNFT v1 #157612 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6N51
- Type
- protein
- Length
- 1,830 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metabotropic glutamate receptor 5; Nanobody 43
- UniProt
- P41594
- Ligands
- QUS, NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Metabotropic glutamate receptor 5 | protein | 793 | 41% helix, 14% strand | P41594 |
| C, D | Nanobody 43 | protein | 123 | 5% helix, 50% strand | — |
| A | Metabotropic glutamate receptor 5 | protein | 791 | 41% helix, 14% strand | P41594 |
Ligands and binding sites
- QUS · (S)-2-amino-3-(3,5-dioxo-[1,2,4]oxadiazolidin-2-yl)-propionic acid · ligand · 2 copies · chains B, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.86 | 0.88 | 94 | QUS |
| 2 | 545 | 0.77 | 0.84 | 57 | empty |
| 3 | 543 | 0.76 | 0.83 | 58 | empty |
| 4 | 645 | 0.76 | 0.82 | 67 | empty |
| 5 | 1023 | 0.76 | 0.78 | 83 | empty |
Interfaces
5 interfaces between chains.
- B–A · 1943 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 827 Ų buried · 11 hydrogen bonds · protein-protein
- C–A · 777 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 103 Ų buried · 2 hydrogen bonds · protein-protein
- D–A · 68 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6N51 · Metabotropic Glutamate Receptor 5 bound to L-quisqualate and Nb43 · the same entry in another collection · chain B against B, 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 0.94
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 6N51 · PDBe 6N51 · UniProt P41594
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