MolNFT v1 · #86671 · protein
Crystal structure of the GLUK2 K531A lbd dimer in complex with kainate
4BDM · Glutamate receptor, ionotropic kainate 2: “Crystal structure of the GLUK2 K531A lbd dimer in complex with kainate”. X-ray diffraction, 1 ligand (KAI), 14 pockets (best druggability 0.80). MolNFT v1 #86671 on GenesisL1: 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.