Research workbench
Crystal structure of the GLUK1 ligand-binding domain (S1S2) in complex with the antagonist (S)-2-amino-3-(2-(2-carboxyethyl)-5-chloro-4- NITROPHENYL)PROPIONIC acid at 2.0 a resolution
Analyse Crystal structure of the GLUK1 ligand-binding domain (S1S2) in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DLD
- Type
- protein
- Length
- 509 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 1
- UniProt
- P22756
- Ligands
- TZG, CL, SO4
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor, ionotropic kainate 1 | protein | 255 | 38% helix, 20% strand | P22756 |
| B | Glutamate receptor, ionotropic kainate 1 | protein | 254 | 38% helix, 20% strand | P22756 |
Ligands and binding sites
- TZG · (S)-2-amino-3-(2-(2-carboxyethyl)-5-chloro-4-nitrophenyl)propionic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · chains 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 | 536 | 0.77 | 0.84 | 63 | TZG |
| 2 | 594 | 0.72 | 0.80 | 71 | empty |
| 3 | 204 | 0.67 | 0.85 | 32 | TZG |
| 4 | 68 | 0.35 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1131 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4DLD · Crystal structure of the GluK1 ligand-binding domain (S1S2) in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
- P22756 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 1 (P22756) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P22756
- Elsewhere: RCSB PDB 4DLD · PDBe 4DLD · UniProt P22756
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