Research workbench
Crystal structure of the GLUK2/GLUK5 (GLUR6/KA2) atd dimer assembly
Analyse Crystal structure of the GLUK2/GLUK5 (GLUR6/KA2) atd dimer assembly in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QLU
- Type
- protein
- Length
- 1,498 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 5; Glutamate receptor, ionotropic kainate 2
- UniProt
- Q63273, P42260
- Ligands
- NAG, CL
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor, ionotropic kainate 5 | protein | 372 | 35% helix, 19% strand | Q63273 |
| B | Glutamate receptor, ionotropic kainate 5 | protein | 381 | 34% helix, 18% strand | Q63273 |
| C | Glutamate receptor, ionotropic kainate 2 | protein | 372 | 35% helix, 24% strand | P42260 |
| D | Glutamate receptor, ionotropic kainate 2 | protein | 373 | 35% helix, 24% strand | P42260 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B, C
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.85 | 0.86 | 107 | empty |
| 2 | 1199 | 0.83 | 0.85 | 109 | empty |
| 3 | 611 | 0.77 | 0.83 | 100 | CL, GOL |
| 4 | 339 | 0.61 | 0.78 | 47 | empty |
| 5 | 220 | 0.58 | 0.80 | 29 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1611 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1552 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 608 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 3QLU · Crystal structure of the GluK2/GluK5 (GluR6/KA2) ATD dimer assembly · the same entry in another collection · chain A against A, TM-score 1.00
- Q63273 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 5 (Q63273) · a predicted model of the same protein · chain A 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 Q63273
- Every structure of UniProt P42260
- Elsewhere: RCSB PDB 3QLU · PDBe 3QLU · UniProt Q63273 · UniProt P42260
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