Research workbench
Crystal structure of the GLUK2 K531A lbd dimer in complex with kainate
Analyse Crystal structure of the GLUK2 K531A 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
- 4BDM
- 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
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor, ionotropic kainate 2 | protein | 246 | 40% helix, 22% strand | P42260 |
| B, C, D | Glutamate receptor, ionotropic kainate 2 | protein | 248 | 40% 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
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.80 | 0.81 | 102 | empty |
| 2 | 1072 | 0.79 | 0.80 | 132 | empty |
| 3 | 723 | 0.73 | 0.79 | 92 | empty |
| 4 | 53 | 0.71 | 0.98 | 13 | empty |
| 5 | 187 | 0.69 | 0.87 | 32 | KAI |
Interfaces
6 interfaces between chains.
- C–D · 1012 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 984 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 637 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 354 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 219 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4BDM · Crystal structure of the GluK2 K531A 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 4BDM · PDBe 4BDM · UniProt P42260
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