Research workbench
cryo-EM structure of homomeric kainate receptor GluK2 in resting (apo) state
Analyse cryo-EM structure of homomeric kainate receptor GluK2 in resting (apo) state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8F0O
- Type
- protein
- Length
- 2,968 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.99
- Source
- Rattus norvegicus
- Molecule
- Glutamate receptor ionotropic, kainate 2
- UniProt
- P42260
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 2.99 · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutamate receptor ionotropic, kainate 2 | protein | 742 | 40% helix, 16% strand | P42260 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.83 | 0.84 | 106 | empty |
| 2 | 1029 | 0.82 | 0.83 | 110 | empty |
| 3 | 968 | 0.78 | 0.80 | 96 | empty |
| 4 | 859 | 0.76 | 0.79 | 63 | empty |
| 5 | 1119 | 0.76 | 0.78 | 91 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3369 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 3344 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1594 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1513 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 537 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- P42260 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 2 (P42260) · a predicted model of the same protein · chain C against A, TM-score 0.84
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 8F0O · PDBe 8F0O · UniProt P42260
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