Research workbench
X-ray structure of the 2-22' locally-closed mutant of glic in complex with thiopental
Analyse X-ray structure of the 2-22' locally-closed mutant of glic in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L4E
- 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
- D12, EDP, CL
- Pockets
- 19 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Proton-gated ion channel | protein | 311 | 36% helix, 33% strand | Q7NDN8 |
Ligands and binding sites
- D12 · Dodecane · ligand · chains A, B, C, D, E
- EDP · 5-ethyl-5-[(2R)-pentan-2-yl]-2-thioxodihydropyrimidine-4,6(1H,5H)-dione · ligand · chains A, B, C, D, E
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.89 | 0.91 | 105 | empty |
| 2 | 532 | 0.85 | 0.91 | 63 | D12, EDP |
| 3 | 461 | 0.85 | 0.92 | 54 | empty |
| 4 | 450 | 0.85 | 0.92 | 53 | empty |
| 5 | 309 | 0.83 | 0.93 | 29 | empty |
Interfaces
10 interfaces between chains.
- C–D · 2324 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2312 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 2289 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 2289 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 2226 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5L4E · X-ray structure of the 2-22' locally-closed mutant of GLIC in complex with thiopental · 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 B against A, TM-score 0.98
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 5L4E · PDBe 5L4E · UniProt Q7NDN8
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