Research workbench
Crystal structure of the kainate receptor GLUR5 ligand-binding core in complex with (S)-glutamate
Analyse Crystal structure of the kainate receptor GLUR5 ligand-binding core in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YCJ
- Type
- protein
- Length
- 507 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ionotropic glutamate receptor 5
- UniProt
- P22756
- Ligands
- GLU, SO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ionotropic glutamate receptor 5 | protein | 251 | 40% helix, 22% strand | P22756 |
| B | Ionotropic glutamate receptor 5 | protein | 256 | 39% helix, 20% strand | P22756 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.78 | 0.80 | 99 | SO4 |
| 2 | 67 | 0.73 | 0.98 | 21 | GLU |
| 3 | 70 | 0.73 | 0.97 | 20 | GLU |
| 4 | 77 | 0.45 | 0.81 | 20 | SO4 |
Interfaces
1 interface between chains.
- A–B · 872 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1YCJ · Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with… · 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 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 P22756
- Elsewhere: RCSB PDB 1YCJ · PDBe 1YCJ · UniProt P22756
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