Research workbench
Crystal structure of the GLUK3 ligand binding domain complex with sym and zinc
Analyse Crystal structure of the GLUK3 ligand binding domain complex with sym and zinc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JMV
- Type
- protein
- Length
- 509 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, kainate 3
- UniProt
- P42264
- Ligands
- SYM, ZN, NA, CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, kainate 3 | protein | 256 | 38% helix, 22% strand | P42264 |
| B | Glutamate receptor ionotropic, kainate 3 | protein | 253 | 38% helix, 22% strand | P42264 |
Ligands and binding sites
- SYM · 2S,4R-4-methylglutamate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 5 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 | 917 | 0.70 | 0.75 | 63 | ACT, GOL |
| 2 | 180 | 0.64 | 0.84 | 39 | SYM, GOL |
| 3 | 203 | 0.64 | 0.83 | 37 | SYM, GOL |
| 4 | 137 | 0.45 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 248 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6JMV · Crystal structure of the GluK3 ligand binding domain complex with SYM and zinc · 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 6JMV · PDBe 6JMV · UniProt P42264
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