MolNFT v1 · #74717 · protein
Structure of propofol bound to a pentameric ligand-gated ion channel, glic
3P50 · GLR4197 protein: “Structure of propofol bound to a pentameric ligand-gated ion channel, glic”. X-ray diffraction, 2 ligands (PLC, PFL), 20 pockets (best druggability 0.81). MolNFT v1 #74717 on GenesisL1: 3D structure, binding sites…
- PDB
- 3P50
- Type
- protein
- Length
- 1,555 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GLR4197 protein
- UniProt
- Q7NDN8
- Ligands
- PLC, PFL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | GLR4197 protein | protein | 311 | 38% helix, 34% strand | Q7NDN8 |
Ligands and binding sites
- PLC · Diundecyl phosphatidyl choline · ligand · 10 copies · chains A, B, C, D, E
- PFL · 2,6-bis(1-methylethyl)phenol · ligand · 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 | 1147 | 0.81 | 0.82 | 60 | LMT |
| 2 | 126 | 0.75 | 0.94 | 27 | empty |
| 3 | 401 | 0.74 | 0.84 | 53 | empty |
| 4 | 369 | 0.73 | 0.84 | 48 | empty |
| 5 | 386 | 0.73 | 0.84 | 47 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2323 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 2314 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 2304 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 2282 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 2261 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3P50 · Structure of propofol bound to a pentameric ligand-gated ion channel, GLIC · 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 3P50 · PDBe 3P50 · UniProt Q7NDN8
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