MolNFT v1 · #178122 · protein
Dnqx-bound GLUK2-1XNETO2 complex
7F59 · Glutamate receptor ionotropic, kainate 2: “Dnqx-bound GLUK2-1XNETO2 complex”. Electron microscopy, 3 ligands (PGT, NAG, BMA), 20 pockets (best druggability 0.84). MolNFT v1 #178122 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7F59
- Type
- protein
- Length
- 3,628 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
- PGT, NAG, BMA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor ionotropic, kainate 2 | protein | 835 | 41% helix, 14% strand | P42260 |
| B | Glutamate receptor ionotropic, kainate 2 | protein | 831 | 40% helix, 14% strand | P42260 |
| D | Glutamate receptor ionotropic, kainate 2 | protein | 818 | 39% helix, 11% strand | P42260 |
| E | Neuropilin and tolloid-like protein 2 | protein | 309 | 8% helix, 29% strand | C6K2K4 |
Ligands and binding sites
- PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · chains C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 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 | 814 | 0.84 | 0.86 | 91 | empty |
| 2 | 348 | 0.83 | 0.92 | 42 | empty |
| 3 | 735 | 0.82 | 0.86 | 96 | empty |
| 4 | 1118 | 0.82 | 0.83 | 116 | empty |
| 5 | 1196 | 0.81 | 0.82 | 103 | empty |
Interfaces
7 interfaces between chains.
- C–D · 3742 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 3659 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 3492 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 3401 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 1328 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 7F59 · DNQX-bound GluK2-1xNeto2 complex · 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 C against A, TM-score 0.58
- 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 0.55
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 7F59 · PDBe 7F59 · UniProt P42260 · UniProt C6K2K4
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