Research workbench
Crystal structure of the ligand-binding core of GLUR5 in complex with the agonist 4-ahcp
Analyse Crystal structure of the ligand-binding core of GLUR5 in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WKY
- Type
- protein
- Length
- 507 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 1
- UniProt
- P22756
- Ligands
- IBC, CL
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor, ionotropic kainate 1 | protein | 254 | 39% helix, 22% strand | P22756 |
| B | Glutamate receptor, ionotropic kainate 1 | protein | 253 | 39% helix, 22% strand | P22756 |
Ligands and binding sites
- IBC · 3-(3-hydroxy-7,8-dihydro-6H-cyclohepta[d]isoxazol-4-yl)-L-alanine · 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
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.77 | 0.81 | 85 | empty |
| 2 | 201 | 0.68 | 0.86 | 31 | IBC |
| 3 | 261 | 0.67 | 0.83 | 41 | IBC |
| 4 | 180 | 0.56 | 0.80 | 30 | empty |
| 5 | 62 | 0.34 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1091 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2WKY · Crystal structure of the ligand-binding core of GluR5 in complex with the agonist 4-AHCP · the same entry in another collection · chain A against A, TM-score 1.00
- P22756 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 1 (P22756) · 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 P22756
- Elsewhere: RCSB PDB 2WKY · PDBe 2WKY · UniProt P22756
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