MolNFT v1 · #95275 · protein
The pentameric ligand-gated ion channel glic A237F in complex with cesium
4ILA · Proton-gated ion channel: “The pentameric ligand-gated ion channel glic A237F in complex with cesium”. X-ray diffraction, 4 ligands (PLC, UNL, CS), 20 pockets (best druggability 0.83). MolNFT v1 #95275 on GenesisL1: 3D structure…
- PDB
- 4ILA
- Type
- protein
- Length
- 1,554 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, CS, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Proton-gated ion channel | protein | 311 | 36% helix, 34% strand | Q7NDN8 |
| E | Proton-gated ion channel | protein | 310 | 36% helix, 34% 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, E, B, C, D
- CS · Cesium ion · metal · 27 copies · chains A, B, C, E, D
- CL · Chloride ion · ion · 5 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 | 1044 | 0.83 | 0.84 | 57 | CS, LMT |
| 2 | 82 | 0.75 | 0.97 | 19 | empty |
| 3 | 540 | 0.71 | 0.80 | 62 | ACT, CS, CL |
| 4 | 371 | 0.71 | 0.83 | 49 | empty |
| 5 | 394 | 0.70 | 0.82 | 46 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2349 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 2347 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 2315 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 2311 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 2294 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4ILA · The pentameric ligand-gated ion channel GLIC A237F in complex with Cesium · 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 A 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 4ILA · PDBe 4ILA · UniProt Q7NDN8
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