Research workbench
The GLIC pentameric Ligand-Gated Ion Channel (wild-type) in complex with bromoacetate
Analyse The GLIC pentameric Ligand-Gated Ion Channel (wild-type) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QH1
- Type
- protein
- Length
- 1,555 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.4
- Source
- Gloeobacter violaceus PCC 7421
- Molecule
- Proton-gated ion channel
- UniProt
- Q7NDN8
- Ligands
- BXA, NA, BR
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · resolution 3.4 · 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
- BXA · bromoacetic acid · ligand · 10 copies · chains A, E, B, C, D
- NA · Sodium ion · metal · chains A, B, E
- BR · Bromide ion · ion · 5 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 | 1165 | 0.81 | 0.81 | 56 | NA |
| 2 | 387 | 0.72 | 0.83 | 54 | empty |
| 3 | 387 | 0.71 | 0.82 | 50 | empty |
| 4 | 519 | 0.71 | 0.80 | 64 | BR, BXA |
| 5 | 415 | 0.71 | 0.82 | 52 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2365 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 2317 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 2315 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2308 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 2263 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4QH1 · The glic pentameric ligand-gated ion channel (wild-type) in complex with bromoacetate · 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 4QH1 · PDBe 4QH1 · UniProt Q7NDN8
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