MolNFT v1 · #115564 · protein
MGLUR2 with glutamate analog
5CNJ · Metabotropic glutamate receptor 2: “MGLUR2 with glutamate analog”. X-ray diffraction, 2 ligands (52Q, NAG), 6 pockets (best druggability 0.82). MolNFT v1 #115564 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CNJ
- Type
- protein
- Length
- 890 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metabotropic glutamate receptor 2
- UniProt
- Q14416
- Ligands
- 52Q, NAG
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metabotropic glutamate receptor 2 | protein | 445 | 37% helix, 21% strand | Q14416 |
| B | Metabotropic glutamate receptor 2 | protein | 445 | 38% helix, 20% strand | Q14416 |
Ligands and binding sites
- 52Q · (1R,2S,4R,5R,6R)-2-amino-4-(1H-1,2,4-triazol-3-ylsulfanyl)bicyclo[3.1.0]hexane-2,6-dicarboxylic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.82 | 0.84 | 106 | 52Q |
| 2 | 569 | 0.75 | 0.82 | 69 | 52Q |
| 3 | 112 | 0.62 | 0.87 | 22 | empty |
| 4 | 134 | 0.61 | 0.85 | 26 | empty |
| 5 | 123 | 0.43 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1022 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- Q14416 · AlphaFold monomer V2.0 prediction for metabotropic glutamate receptor 2 (Q14416) · a predicted model of the same protein · chain B 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 Q14416
- Elsewhere: RCSB PDB 5CNJ · PDBe 5CNJ · UniProt Q14416
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