Research workbench
Structure of the kainate receptor subunit GLUR6 agonist binding domain complexed with domoic acid
Analyse Structure of the kainate receptor subunit GLUR6 agonist binding domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YAE
- Type
- protein
- Length
- 1,521 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 2
- Ligands
- DOQ, NAG, FUC
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor, ionotropic kainate 2 | protein | 261 | 38% helix, 24% strand | — |
| B | Glutamate receptor, ionotropic kainate 2 | protein | 261 | 38% helix, 22% strand | — |
| C | Glutamate receptor, ionotropic kainate 2 | protein | 257 | 39% helix, 21% strand | — |
| D | Glutamate receptor, ionotropic kainate 2 | protein | 259 | 38% helix, 23% strand | — |
| E | Glutamate receptor, ionotropic kainate 2 | protein | 257 | 36% helix, 21% strand | — |
| F | Glutamate receptor, ionotropic kainate 2 | protein | 226 | 35% helix, 20% strand | — |
Ligands and binding sites
- DOQ · (2S,3S,4S)-2-carboxy-4-[(1Z,3E,5R)-5-carboxy-1-methyl-1,3-hexadienyl]-3-pyrrolidineacetic acid · ligand · 6 copies · chains A, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D, E, F
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 711 | 0.83 | 0.87 | 74 | DOQ |
| 2 | 864 | 0.82 | 0.85 | 81 | DOQ |
| 3 | 863 | 0.79 | 0.82 | 88 | empty |
| 4 | 415 | 0.73 | 0.84 | 54 | DOQ |
| 5 | 202 | 0.71 | 0.88 | 33 | DOQ |
Interfaces
9 interfaces between chains.
- B–D · 1459 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 855 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 606 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 576 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 554 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 1YAE · Structure of the Kainate Receptor Subunit GluR6 Agonist Binding Domain Complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1YAE · PDBe 1YAE
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