MolNFT v1 · #54727 · protein
Crystal structure of the GLUK2 (GLUR6) D776K lbd dimer in complex with kainate
2XXY · Glutamate receptor, ionotropic kainate 2: “Crystal structure of the GLUK2 (GLUR6) D776K lbd dimer in complex with kainate”. X-ray diffraction, 1 ligand (KAI), 17 pockets (best druggability 0.78). MolNFT v1 #54727 on GenesisL1: 3D…
- PDB
- 2XXY
- Type
- protein
- Length
- 990 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 2
- UniProt
- P42260
- Ligands
- KAI
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glutamate receptor, ionotropic kainate 2 | protein | 248 | 40% helix, 21% strand | P42260 |
| D | Glutamate receptor, ionotropic kainate 2 | protein | 246 | 38% helix, 22% strand | P42260 |
Ligands and binding sites
- KAI · 3-(carboxymethyl)-4-isopropenylproline · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.78 | 0.80 | 140 | empty |
| 2 | 786 | 0.74 | 0.79 | 67 | empty |
| 3 | 60 | 0.70 | 0.97 | 13 | empty |
| 4 | 155 | 0.66 | 0.87 | 31 | KAI |
| 5 | 145 | 0.66 | 0.87 | 32 | KAI |
Interfaces
6 interfaces between chains.
- C–D · 1198 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1150 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 639 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 306 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 188 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2XXY · Crystal structure of the GluK2 (GluR6) D776K LBD dimer in complex with kainate · the same entry in another collection · chain D against D, 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 D 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 2XXY · PDBe 2XXY · UniProt P42260
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