Research workbench
X-ray structure of the F14'A mutant of glic in complex with propofol
Analyse X-ray structure of the F14'A mutant of glic in complex with propofol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MUR
- 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, PFL, NA, CL
- Pockets
- 20 · best druggability 0.80
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 · 5 copies · chains A, B, C, D, E
- PFL · 2,6-bis(1-methylethyl)phenol · ligand · 2 copies · chains B, E
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D, E
- ACT · Acetate ion · additive · 10 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 | 1136 | 0.80 | 0.81 | 61 | NA |
| 2 | 84 | 0.75 | 0.97 | 22 | empty |
| 3 | 93 | 0.73 | 0.95 | 22 | empty |
| 4 | 91 | 0.72 | 0.95 | 23 | empty |
| 5 | 86 | 0.72 | 0.95 | 23 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2302 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 2295 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 2278 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 2277 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 2274 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5MUR · X-ray structure of the F14'A mutant of GLIC in complex with propofol · 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 5MUR · PDBe 5MUR · UniProt Q7NDN8
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