MolNFT v1 · #101597 · protein
Crystal structure of the kainate receptor GLUK3 ligand-binding domain in complex with the agonist (2S,4R)-4-(3-methylamino-3-oxopropyl) glutamic acid at 2.6 a resolution
4NWD · Glutamate receptor ionotropic, kainate 3: “Crystal structure of the kainate receptor GLUK3 ligand-binding domain in complex with the agonist…”. X-ray diffraction, 3 ligands (2QD, K, CL), 3 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 4NWD
- Type
- protein
- Length
- 254 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, kainate 3
- UniProt
- P42264
- Ligands
- 2QD, K, CL
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, kainate 3 | protein | 254 | 35% helix, 21% strand | P42264 |
Ligands and binding sites
- 2QD · (4R)-4-[3-(methylamino)-3-oxopropyl]-L-glutamic acid · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.72 | 0.97 | 20 | 2QD |
| 2 | 114 | 0.45 | 0.78 | 26 | empty |
| 3 | 99 | 0.40 | 0.77 | 23 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4NWD · Crystal structure of the kainate receptor GluK3 ligand-binding domain in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
- P42264 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 3 (P42264) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P42264
- Elsewhere: RCSB PDB 4NWD · PDBe 4NWD · UniProt P42264
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