MolNFT v1 · #86670 · protein
Crystal structure of the GLUK2 K531A lbd dimer in complex with glutamate
4BDL · Glutamate receptor, ionotropic kainate 2: “Crystal structure of the GLUK2 K531A lbd dimer in complex with glutamate”. X-ray diffraction, 2 ligands (GLU, NA), 4 pockets (best druggability 0.77). MolNFT v1 #86670 on GenesisL1: 3D…
- PDB
- 4BDL
- 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
- GLU, NA
- Pockets
- 4 · 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 | 249 | 39% helix, 22% strand | P42260 |
| B | Glutamate receptor, ionotropic kainate 2 | protein | 248 | 40% helix, 22% strand | P42260 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.77 | 0.80 | 114 | empty |
| 2 | 185 | 0.61 | 0.83 | 38 | GLU |
| 3 | 113 | 0.58 | 0.85 | 30 | GLU |
| 4 | 60 | 0.35 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 920 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4BDL · Crystal structure of the GluK2 K531A LBD dimer in complex with glutamate · the same entry in another collection · chain B against B, 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 0.97
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 4BDL · PDBe 4BDL · UniProt P42260
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