Research workbench
Crystal structure of the ligand-binding core of IGLUR5 in complex with the partial agonist domoic acid at 2.5 a resolution
Analyse Crystal structure of the ligand-binding core of IGLUR5 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
- 2PBW
- Type
- protein
- Length
- 501 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 1
- UniProt
- P22756
- Ligands
- DOQ
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor, ionotropic kainate 1 | protein | 248 | 39% helix, 21% strand | P22756 |
| B | Glutamate receptor, ionotropic kainate 1 | protein | 253 | 39% helix, 21% strand | P22756 |
Ligands and binding sites
- DOQ · (2S,3S,4S)-2-carboxy-4-[(1Z,3E,5R)-5-carboxy-1-methyl-1,3-hexadienyl]-3-pyrrolidineacetic acid · ligand · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.74 | 0.81 | 72 | empty |
| 2 | 333 | 0.69 | 0.82 | 44 | DOQ |
| 3 | 309 | 0.69 | 0.83 | 39 | DOQ |
| 4 | 156 | 0.49 | 0.78 | 22 | empty |
| 5 | 157 | 0.48 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1182 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2PBW · Crystal Structure of the Ligand-Binding Core of iGluR5 in Complex with the Partial… · the same entry in another collection · chain B against B, 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 0.99
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 2PBW · PDBe 2PBW · UniProt P22756
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