MolNFT v1 · #67312 · protein
Crystal structure of the extracellular domain of a bacterial pentameric ligand-gated ion channel
3IGQ · GLR4197 protein: “Crystal structure of the extracellular domain of a bacterial pentameric ligand-gated ion channel”. X-ray diffraction, 3 ligands (NA, HG, CL), 17 pockets (best druggability 0.64). MolNFT v1 #67312 on GenesisL1: 3D…
- PDB
- 3IGQ
- Type
- protein
- Length
- 1,075 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GLR4197 protein
- UniProt
- Q7NDN8
- Ligands
- NA, HG, CL
- Pockets
- 17 · best druggability 0.64
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GLR4197 protein | protein | 176 | 7% helix, 55% strand | Q7NDN8 |
| B | GLR4197 protein | protein | 180 | 7% helix, 53% strand | Q7NDN8 |
| C | GLR4197 protein | protein | 184 | 7% helix, 51% strand | Q7NDN8 |
| D | GLR4197 protein | protein | 174 | 7% helix, 53% strand | Q7NDN8 |
| E | GLR4197 protein | protein | 180 | 7% helix, 53% strand | Q7NDN8 |
| F | GLR4197 protein | protein | 181 | 7% helix, 54% strand | Q7NDN8 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E, F
- HG · Mercury (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
- ACY · Acetic acid · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.64 | 0.81 | 41 | empty |
| 2 | 64 | 0.58 | 0.89 | 21 | empty |
| 3 | 50 | 0.58 | 0.90 | 13 | empty |
| 4 | 55 | 0.52 | 0.87 | 20 | empty |
| 5 | 124 | 0.50 | 0.80 | 28 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1262 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1209 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1181 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1051 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3IGQ · Crystal structure of the extracellular domain of a bacterial pentameric ligand-gated ion… · the same entry in another collection · chain F against F, 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 0.95
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 3IGQ · PDBe 3IGQ · UniProt Q7NDN8
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