MolNFT v1 · #91278 · protein
X-ray structure of the anesthetic ketamine bound to the glic pentameric ligand-gated ion channel
4F8H · Proton-gated ion channel: “X-ray structure of the anesthetic ketamine bound to the glic pentameric ligand-gated ion channel”. X-ray diffraction, 3 ligands (PC1, LMD, RKE), 20 pockets (best druggability 0.81). MolNFT v1 #91278 on…
- PDB
- 4F8H
- 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
- PC1, LMD, RKE
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Proton-gated ion channel | protein | 311 | 36% helix, 35% strand | Q7NDN8 |
Ligands and binding sites
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 10 copies · chains A, E, B, C, D
- LMD · tetradecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside · ligand · 6 copies · chains A, B, E, C, D
- RKE · (R)-ketamine · ligand · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.81 | 0.82 | 62 | LMD |
| 2 | 398 | 0.72 | 0.83 | 51 | empty |
| 3 | 373 | 0.72 | 0.84 | 47 | empty |
| 4 | 376 | 0.72 | 0.83 | 50 | empty |
| 5 | 408 | 0.71 | 0.82 | 53 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2277 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2267 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2263 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 2260 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 2256 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4F8H · X-ray Structure of the Anesthetic Ketamine Bound to the GLIC Pentameric Ligand-gated Ion… · 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 4F8H · PDBe 4F8H · UniProt Q7NDN8
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