Research workbench
Crystal structure of the GLUK2 R775A lbd dimer in complex with kainate
Analyse Crystal structure of the GLUK2 R775A lbd dimer in complex with kainate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BDR
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 2
- UniProt
- P42260
- Ligands
- KAI, NA, CL
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor, ionotropic kainate 2 | protein | 253 | 39% helix, 21% strand | P42260 |
| B | Glutamate receptor, ionotropic kainate 2 | protein | 249 | 39% helix, 22% strand | P42260 |
Ligands and binding sites
- KAI · 3-(carboxymethyl)-4-isopropenylproline · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 813 | 0.76 | 0.80 | 85 | empty |
| 2 | 168 | 0.69 | 0.88 | 32 | KAI |
| 3 | 180 | 0.67 | 0.86 | 32 | KAI |
| 4 | 185 | 0.56 | 0.80 | 29 | empty |
| 5 | 58 | 0.43 | 0.83 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1044 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4BDR · Crystal structure of the GluK2 R775A LBD dimer in complex with kainate · the same entry in another collection · chain A against A, TM-score 1.00
- P42260 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 2 (P42260) · 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 P42260
- Elsewhere: RCSB PDB 4BDR · PDBe 4BDR · UniProt P42260
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