Research workbench
Structure of the ligand-binding core of GLUR2 in complex with the agonist (S)-tdpa at 2.25 a resolution
Analyse Structure of the ligand-binding core of GLUR2 in complex with the agonist… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BFT
- Type
- protein
- Length
- 777 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- S2P, ZN, NA, CL
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glutamate receptor 2 | protein | 259 | 37% helix, 21% strand | P19491 |
Ligands and binding sites
- S2P · (2S)-2-amino-3-(4-hydroxy-1,2,5-thiadiazol-3-yl)propanoic acid · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 5 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- CAC · Cacodylate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.72 | 0.81 | 71 | empty |
| 2 | 60 | 0.70 | 0.97 | 19 | S2P |
| 3 | 50 | 0.69 | 0.98 | 20 | S2P |
| 4 | 204 | 0.60 | 0.81 | 34 | empty |
| 5 | 280 | 0.59 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–C · 998 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3BFT · Structure of the ligand-binding core of GluR2 in complex with the agonist (S)-TDPA at… · the same entry in another collection · chain C against C, TM-score 1.00
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain C 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 P19491
- Elsewhere: RCSB PDB 3BFT · PDBe 3BFT · UniProt P19491
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