MolNFT v1 · #28310 · protein
Structure of the kainate receptor subunit GLUR6 agonist binding domain complexed with domoic acid
1YAE · Glutamate receptor, ionotropic kainate 2: “Structure of the kainate receptor subunit GLUR6 agonist binding domain complexed with domoic acid”. X-ray diffraction, 3 ligands (DOQ, NAG, FUC), 20 pockets (best druggability 0.83). MolNFT…
- 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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