Research workbench
The glic pentameric ligand-gated ion channel (wild-type) crystallized in phosphate buffer
Analyse The glic pentameric ligand-gated ion channel (wild-type) crystallized in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QH5
- 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, NA, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Proton-gated ion channel | protein | 311 | 36% helix, 34% strand | Q7NDN8 |
Ligands and binding sites
- PLC · Diundecyl phosphatidyl choline · ligand · 2 copies · chains C, E
- NA · Sodium ion · metal · 4 copies · chains B, A, C, D, E
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D, E
- LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, B, E, C, D
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 | 1132 | 0.82 | 0.82 | 61 | LMT, NA |
| 2 | 379 | 0.72 | 0.83 | 47 | empty |
| 3 | 368 | 0.72 | 0.84 | 51 | empty |
| 4 | 95 | 0.69 | 0.93 | 25 | empty |
| 5 | 107 | 0.69 | 0.92 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2374 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2295 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 2286 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 2281 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 2252 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4QH5 · The GLIC pentameric Ligand-Gated Ion Channel (wild-type) crystallized in phosphate buffer · 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 D 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 4QH5 · PDBe 4QH5 · UniProt Q7NDN8
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