MolNFT v1 · #178354 · protein
Thermostabilised full length human MGLUR5-5M with orthosteric antagonist, LY341495
7FD9 · Metabotropic glutamate receptor 5: “Thermostabilised full length human MGLUR5-5M with orthosteric antagonist, LY341495”. Electron microscopy, 2 ligands (Z99, NAG), 16 pockets (best druggability 0.77). MolNFT v1 #178354 on GenesisL1…
- PDB
- 7FD9
- Type
- protein
- Length
- 1,534 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metabotropic glutamate receptor 5
- UniProt
- P41594
- Ligands
- Z99, NAG
- Pockets
- 16 · best druggability 0.77
Structure
electron microscopy · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metabotropic glutamate receptor 5 | protein | 767 | 45% helix, 14% strand | P41594 |
Ligands and binding sites
- Z99 · 2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.77 | 0.93 | 30 | empty |
| 2 | 166 | 0.77 | 0.93 | 33 | empty |
| 3 | 242 | 0.73 | 0.88 | 39 | empty |
| 4 | 234 | 0.73 | 0.88 | 39 | empty |
| 5 | 695 | 0.71 | 0.78 | 71 | empty |
Interfaces
1 interface between chains.
- A–B · 727 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7FD9 · Thermostabilised full length human mGluR5-5M with orthosteric antagonist, LY341495 · 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 A against A, TM-score 0.87
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 7FD9 · PDBe 7FD9 · UniProt P41594
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