Research workbench
Crystal structure of the extracellular region of the group II metabotropic glutamate receptor complexed with 2R,4R-apdc
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
- 2E4Y
- Type
- protein
- Length
- 977 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metabotropic glutamate receptor 3
- UniProt
- P31422
- Ligands
- 52A, NAG
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metabotropic glutamate receptor 3 | protein | 518 | 30% helix, 20% strand | P31422 |
| B | Metabotropic glutamate receptor 3 | protein | 459 | 33% helix, 19% strand | P31422 |
Ligands and binding sites
- 52A · (2R,4R)-4-aminopyrrolidine-2,4-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
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.72 | 0.88 | 32 | empty |
| 2 | 221 | 0.71 | 0.87 | 32 | empty |
| 3 | 412 | 0.66 | 0.80 | 50 | empty |
| 4 | 390 | 0.65 | 0.79 | 49 | empty |
| 5 | 301 | 0.62 | 0.80 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 633 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2E4Y · Crystal structure of the extracellular region of the group II metabotropic glutamate… · the same entry in another collection · chain B against B, TM-score 1.00
- P31422 · AlphaFold monomer V2.0 prediction for metabotropic glutamate receptor 3 (P31422) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 2E4Y · PDBe 2E4Y · UniProt P31422
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