MolNFT v1 · #147205 · protein
Human MGLU8 receptor amino terminal domain in complex with (S)-3,4- dicarboxyphenylglycine (dcpg)
6E5V · Metabotropic glutamate receptor 8: “Human MGLU8 receptor amino terminal domain in complex with (S)-3,4- dicarboxyphenylglycine (dcpg)”. X-ray diffraction, 2 ligands (HVG, CL), 9 pockets (best druggability 0.74). MolNFT v1 #147205 on…
- PDB
- 6E5V
- Type
- protein
- Length
- 882 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metabotropic glutamate receptor 8
- UniProt
- O00222
- Ligands
- HVG, CL
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metabotropic glutamate receptor 8 | protein | 435 | 34% helix, 21% strand | O00222 |
| B | Metabotropic glutamate receptor 8 | protein | 447 | 34% helix, 21% strand | O00222 |
Ligands and binding sites
- HVG · 4-[(S)-amino(carboxy)methyl]benzene-1,2-dicarboxylic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.74 | 0.80 | 62 | HVG, CL |
| 2 | 628 | 0.73 | 0.80 | 60 | HVG, CL |
| 3 | 88 | 0.53 | 0.84 | 15 | empty |
| 4 | 79 | 0.51 | 0.84 | 15 | empty |
| 5 | 144 | 0.47 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 747 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6E5V · human mGlu8 receptor amino terminal domain in complex with (S)-3,4-Dicarboxyphenylglycine… · the same entry in another collection · chain A against A, TM-score 1.00
- O00222 · AlphaFold monomer V2.0 prediction for metabotropic glutamate receptor 8 (O00222) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O00222
- Elsewhere: RCSB PDB 6E5V · PDBe 6E5V · UniProt O00222
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