Research workbench
Crystal structure of the kainate receptor GLUK3 ligand binding domain in complex with (S)-glutamate
Analyse Crystal structure of the kainate receptor GLUK3 ligand binding domain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S9E
- Type
- protein
- Length
- 506 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 3
- UniProt
- P42264
- Ligands
- GLU, NA, CL, PO4
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate receptor, ionotropic kainate 3 | protein | 253 | 37% helix, 24% strand | P42264 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.82 | 0.89 | 50 | empty |
| 2 | 97 | 0.70 | 0.93 | 28 | GLU |
| 3 | 86 | 0.67 | 0.92 | 30 | GLU |
| 4 | 199 | 0.56 | 0.79 | 33 | empty |
| 5 | 136 | 0.38 | 0.73 | 27 | CL |
Interfaces
1 interface between chains.
- A–B · 997 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3S9E · Crystal structure of the kainate receptor GluK3 ligand binding domain in complex with… · the same entry in another collection · chain B against B, 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 0.95
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 3S9E · PDBe 3S9E · UniProt P42264
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