MolNFT v1 · #80840 · protein
Crystal structure of the GLUK3 ligand binding domain complex with glutamate and zinc: P2221 form
3U93 · Glutamate receptor, ionotropic kainate 3: “Crystal structure of the GLUK3 ligand binding domain complex with glutamate and zinc: P2221 form”. X-ray diffraction, 3 ligands (GLU, ZN, CL), 6 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 3U93
- Type
- protein
- Length
- 502 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, ZN, CL
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor, ionotropic kainate 3 | protein | 252 | 38% helix, 23% strand | P42264 |
| B | Glutamate receptor, ionotropic kainate 3 | protein | 250 | 38% helix, 22% strand | P42264 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 5 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.72 | 0.97 | 18 | GLU |
| 2 | 57 | 0.70 | 0.98 | 20 | GLU |
| 3 | 862 | 0.70 | 0.75 | 59 | empty |
| 4 | 125 | 0.44 | 0.77 | 29 | empty |
| 5 | 83 | 0.43 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 266 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3U93 · Crystal structure of the GluK3 ligand binding domain complex with glutamate and zinc… · 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 B 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 3U93 · PDBe 3U93 · UniProt P42264
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