MolNFT v1 · #178119 · protein
Dnqx-bound GLUK2-1XNETO2 complex, with asymmetric lbd
7F56 · Glutamate receptor ionotropic, kainate 2: “Dnqx-bound GLUK2-1XNETO2 complex, with asymmetric lbd”. Electron microscopy, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.88). MolNFT v1 #178119 on GenesisL1: 3D structure, binding…
- PDB
- 7F56
- 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 0.88
Structure
electron microscopy · 4 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate receptor ionotropic, kainate 2 | protein | 831 | 41% helix, 15% strand | P42260 |
| C | Glutamate receptor ionotropic, kainate 2 | protein | 835 | 40% helix, 12% strand | P42260 |
| D | Glutamate receptor ionotropic, kainate 2 | protein | 818 | 40% helix, 11% strand | P42260 |
| E | Neuropilin and tolloid-like protein 2 | protein | 153 | 21% helix, 27% strand | C6K2K4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains B, A, D, C
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains B, A, 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 | 1146 | 0.88 | 0.88 | 148 | empty |
| 2 | 893 | 0.83 | 0.85 | 131 | empty |
| 3 | 998 | 0.83 | 0.84 | 100 | empty |
| 4 | 980 | 0.82 | 0.83 | 95 | empty |
| 5 | 1181 | 0.75 | 0.77 | 127 | empty |
Interfaces
8 interfaces between chains.
- C–D · 4024 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 3709 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 3269 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 2312 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 730 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 7F56 · DNQX-bound GluK2-1xNeto2 complex, with asymmetric LBD · 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 0.75
- 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 7F56 · PDBe 7F56 · UniProt P42260 · UniProt C6K2K4
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