Research workbench
The pentameric ligand-gated ion channel glic A237F in complex with bromide
Analyse The pentameric ligand-gated ion channel glic A237F in complex with bromide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IL9
- Type
- protein
- Length
- 1,555 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proton-gated ion channel
- UniProt
- Q7NDN8
- Ligands
- PLC, UNL, NA, BR
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Proton-gated ion channel | protein | 311 | 37% helix, 35% strand | Q7NDN8 |
Ligands and binding sites
- PLC · Diundecyl phosphatidyl choline · ligand · 10 copies · chains A, B, C, D, E
- UNL · Unknown ligand · ligand · 10 copies · chains A, B, C, D, E
- NA · Sodium ion · metal · 6 copies · chains B, C, D, A, E
- BR · Bromide ion · ion · 12 copies · chains A, B, C, D, E
- ACT · Acetate ion · additive · 10 copies · chains A, E, B, C, D
- LMT · Dodecyl-beta-D-maltoside · additive · 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 | 1023 | 0.83 | 0.83 | 55 | LMT, NA |
| 2 | 400 | 0.72 | 0.83 | 46 | empty |
| 3 | 537 | 0.71 | 0.80 | 65 | ACT, BR, NA |
| 4 | 366 | 0.71 | 0.83 | 50 | empty |
| 5 | 373 | 0.70 | 0.83 | 45 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2372 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2352 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2337 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 2336 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 2332 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4IL9 · The pentameric ligand-gated ion channel GLIC A237F in complex with bromide · the same entry in another collection · chain E against E, TM-score 1.00
- Q7NDN8 · AlphaFold monomer V2.0 prediction for proton-gated ion channel (Q7NDN8) · a predicted model of the same protein · chain C 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
- Every structure of UniProt Q7NDN8
- Elsewhere: RCSB PDB 4IL9 · PDBe 4IL9 · UniProt Q7NDN8
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