MolNFT v1 · #157608 · protein
Metabotropic glutamate receptor 5 apo form ligand binding domain
6N4X: “Metabotropic glutamate receptor 5 apo form ligand binding domain”. X-ray diffraction, 2 ligands (NAG, MG), 9 pockets (best druggability 0.66). MolNFT v1 #157608 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6N4X
- Type
- protein
- Length
- 993 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metabotropic glutamate receptor 5
- UniProt
- P41594
- Ligands
- NAG, MG
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metabotropic glutamate receptor 5 | protein | 506 | 34% helix, 17% strand | P41594 |
| B | Metabotropic glutamate receptor 5 | protein | 487 | 34% helix, 18% strand | P41594 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.66 | 0.86 | 42 | empty |
| 2 | 521 | 0.64 | 0.76 | 43 | empty |
| 3 | 384 | 0.59 | 0.76 | 41 | empty |
| 4 | 50 | 0.59 | 0.92 | 20 | empty |
| 5 | 222 | 0.51 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 263 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6N4X · Metabotropic Glutamate Receptor 5 Apo Form Ligand Binding Domain · 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 0.91
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 6N4X · PDBe 6N4X · UniProt P41594
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