Research workbench
Crystal structure of the extracellular region of the group II metabotropic glutamate receptor complexed with 1S,3R-acpd
Analyse Crystal structure of the extracellular region of the group II metabotropic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E4X
- Type
- protein
- Length
- 1,038 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metabotropic glutamate receptor 3
- UniProt
- P31422
- Ligands
- C5B, NAG
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metabotropic glutamate receptor 3 | protein | 518 | 31% helix, 21% strand | P31422 |
| B | Metabotropic glutamate receptor 3 | protein | 520 | 30% helix, 21% strand | P31422 |
Ligands and binding sites
- C5B · (1S,3R)-1-aminocyclopentane-1,3-dicarboxylic acid · 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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.78 | 0.84 | 94 | C5B |
| 2 | 485 | 0.76 | 0.84 | 73 | C5B |
| 3 | 212 | 0.66 | 0.84 | 34 | empty |
| 4 | 191 | 0.65 | 0.85 | 30 | empty |
| 5 | 135 | 0.53 | 0.81 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 705 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2E4X · Crystal structure of the extracellular region of the group II metabotropic glutamate… · the same entry in another collection · chain A against A, TM-score 1.00
- P31422 · AlphaFold monomer V2.0 prediction for metabotropic glutamate receptor 3 (P31422) · 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 P31422
- Elsewhere: RCSB PDB 2E4X · PDBe 2E4X · UniProt P31422
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