MolNFT v1 · #54724 · protein
Crystal structure of the GLUK2 (GLUR6) M770K lbd dimer in complex with kainate
2XXV · Glutamate receptor, ionotropic kainate 2: “Crystal structure of the GLUK2 (GLUR6) M770K lbd dimer in complex with kainate”. X-ray diffraction, 2 ligands (KAI, CL), 5 pockets (best druggability 0.77). MolNFT v1 #54724 on GenesisL1…
- PDB
- 2XXV
- Type
- protein
- Length
- 497 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, 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 2 | protein | 248 | 40% helix, 22% 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
- CL · Chloride ion · ion · 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 | 893 | 0.77 | 0.80 | 105 | empty |
| 2 | 185 | 0.69 | 0.87 | 33 | KAI |
| 3 | 173 | 0.67 | 0.87 | 32 | KAI |
| 4 | 73 | 0.34 | 0.75 | 15 | empty |
| 5 | 61 | 0.31 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1072 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2XXV · Crystal structure of the GluK2 (GluR6) M770K 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 2XXV · PDBe 2XXV · UniProt P42260
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