Research workbench
Crystal structure of the GLUK2 K531A-T779G lbd dimer in complex with kainate
Analyse Crystal structure of the GLUK2 K531A-T779G 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
- 4BDO
- Type
- protein
- Length
- 975 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, NA
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor, ionotropic kainate 2 | protein | 242 | 40% helix, 25% strand | P42260 |
| B | Glutamate receptor, ionotropic kainate 2 | protein | 245 | 40% helix, 22% strand | P42260 |
| C | Glutamate receptor, ionotropic kainate 2 | protein | 246 | 39% helix, 23% strand | P42260 |
| D | Glutamate receptor, ionotropic kainate 2 | protein | 242 | 39% helix, 21% strand | P42260 |
Ligands and binding sites
- KAI · 3-(carboxymethyl)-4-isopropenylproline · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.85 | 0.88 | 121 | empty |
| 2 | 424 | 0.76 | 0.85 | 68 | empty |
| 3 | 56 | 0.72 | 0.99 | 13 | empty |
| 4 | 163 | 0.67 | 0.87 | 31 | KAI |
| 5 | 235 | 0.66 | 0.84 | 40 | KAI |
Interfaces
6 interfaces between chains.
- A–B · 1050 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1037 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 587 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 251 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 203 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 4BDO · Crystal structure of the GluK2 K531A-T779G 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 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 P42260
- Elsewhere: RCSB PDB 4BDO · PDBe 4BDO · UniProt P42260
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