MolNFT v1 · #64449 · protein
Crystal structure of the GLUR6 ligand binding domain dimer I442H K494E K665R I749L Q753K E757Q mutant with glutamate and nacl at 1.24 ångström resolution
3G3K · Glutamate receptor, ionotropic kainate 2: “Crystal structure of the GLUR6 ligand binding domain dimer I442H K494E K665R I749L Q753K E757Q mutant with…”. X-ray diffraction, 3 ligands (GLU, NA, CL), 5 pockets (best druggability 0.78).…
- PDB
- 3G3K
- Type
- protein
- Length
- 509 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 2
- UniProt
- P42260
- Ligands
- GLU, NA, CL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor, ionotropic kainate 2 | protein | 254 | 40% helix, 22% strand | P42260 |
| B | Glutamate receptor, ionotropic kainate 2 | protein | 255 | 40% helix, 22% strand | P42260 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.78 | 0.84 | 79 | CL, IPA |
| 2 | 122 | 0.42 | 0.76 | 25 | empty |
| 3 | 99 | 0.40 | 0.76 | 17 | empty |
| 4 | 95 | 0.37 | 0.75 | 25 | IPA |
| 5 | 64 | 0.31 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1227 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3G3K · Crystal structure of the GluR6 ligand binding domain dimer I442H K494E K665R I749L Q753K… · the same entry in another collection · chain A against A, TM-score 1.00
- P42260 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 2 (P42260) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P42260
- Elsewhere: RCSB PDB 3G3K · PDBe 3G3K · UniProt P42260
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