Research workbench
Crystal structure of the GLUK3 ligand binding domain complex with kainate and zinc: P2221 form
Analyse Crystal structure of the GLUK3 ligand binding domain complex with kainate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U92
- Type
- protein
- Length
- 508 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 3
- UniProt
- P42264
- Ligands
- KAI, ZN, CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate receptor, ionotropic kainate 3 | protein | 254 | 37% helix, 21% strand | P42264 |
Ligands and binding sites
- KAI · 3-(carboxymethyl)-4-isopropenylproline · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B
- CL · Chloride ion · ion · 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 | 896 | 0.70 | 0.76 | 67 | empty |
| 2 | 272 | 0.70 | 0.85 | 41 | KAI |
| 3 | 242 | 0.69 | 0.85 | 38 | KAI |
| 4 | 68 | 0.36 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 306 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3U92 · Crystal structure of the GluK3 ligand binding domain complex with kainate and zinc: P2221… · 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 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 P42264
- Elsewhere: RCSB PDB 3U92 · PDBe 3U92 · UniProt P42264
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