Research workbench
Kainate-bound GLUK2-1XNETO2 complex, at the desensitized state
Analyse Kainate-bound GLUK2-1XNETO2 complex, at the desensitized state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F57
- Type
- protein
- Length
- 3,468 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, kainate 2; Neuropilin and tolloid-like protein 2
- UniProt
- P42260, C6K2K4
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glutamate receptor ionotropic, kainate 2 | protein | 835 | 42% helix, 13% strand | P42260 |
| D | Glutamate receptor ionotropic, kainate 2 | protein | 818 | 39% helix, 14% strand | P42260 |
| E | Neuropilin and tolloid-like protein 2 | protein | 145 | 17% helix, 29% strand | C6K2K4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, B, C, D, E
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B, C, D, E
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 | 431 | 0.84 | 0.92 | 53 | empty |
| 2 | 866 | 0.81 | 0.84 | 102 | empty |
| 3 | 1159 | 0.80 | 0.81 | 123 | empty |
| 4 | 539 | 0.71 | 0.79 | 46 | empty |
| 5 | 52 | 0.69 | 0.96 | 21 | empty |
Interfaces
8 interfaces between chains.
- A–B · 4350 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 4243 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 2397 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 2290 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 912 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 7F57 · Kainate-bound GluK2-1xNeto2 complex, at the desensitized state · the same entry in another collection · chain E against E, 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 0.77
- C6K2K4 · AlphaFold monomer V2.0 prediction for neuropilin and tolloid-like protein 2 (C6K2K4) · a predicted model of the same protein · chain E against A, TM-score 0.68
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
- Every structure of UniProt C6K2K4
- Elsewhere: RCSB PDB 7F57 · PDBe 7F57 · UniProt P42260 · UniProt C6K2K4
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