MolNFT v1 · #127406 · protein
X-ray structure of the M205W mutant of glic in complex with propofol
5MVN · Proton-gated ion channel: “X-ray structure of the M205W mutant of glic in complex with propofol”. X-ray diffraction, 4 ligands (PLC, PFL, NA), 20 pockets (best druggability 0.80). MolNFT v1 #127406 on GenesisL1: 3D structure…
- PDB
- 5MVN
- 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 · 38% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Proton-gated ion channel | protein | 311 | 38% helix, 33% strand | Q7NDN8 |
Ligands and binding sites
- PLC · Diundecyl phosphatidyl choline · ligand · 15 copies · chains A, B, E, C, D
- PFL · 2,6-bis(1-methylethyl)phenol · ligand · 4 copies · chains B, C, D, E
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D, E
- ACT · Acetate ion · additive · 10 copies · chains A, E, B, C, D
- LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, B, C, E, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.80 | 0.81 | 57 | NA, LMT |
| 2 | 589 | 0.78 | 0.84 | 66 | PFL |
| 3 | 539 | 0.78 | 0.84 | 62 | PFL |
| 4 | 397 | 0.72 | 0.83 | 47 | empty |
| 5 | 388 | 0.72 | 0.83 | 54 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2367 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 2365 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2343 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 2328 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 2321 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5MVN · X-ray structure of the M205W 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 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 5MVN · PDBe 5MVN · UniProt Q7NDN8
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