MolNFT v1 · #153705 · protein
Crystal structure of the GLUK3 ligand binding domain complex with sym and zinc
6JMV · Glutamate receptor ionotropic, kainate 3: “Crystal structure of the GLUK3 ligand binding domain complex with sym and zinc”. X-ray diffraction, 4 ligands (SYM, ZN, NA), 4 pockets (best druggability 0.70). MolNFT v1 #153705 on…
- 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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