Research workbench
X-ray structure of the 2-22' locally-closed mutant of glic in complex with 5-(2-bromo-ethyl)-5-ethyl-pyrimidine-2,4,6-trione (brominated barbiturate)
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
- 5L4H
- 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
- 6JW, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Proton-gated ion channel | protein | 311 | 35% helix, 34% strand | Q7NDN8 |
Ligands and binding sites
- 6JW · 5-(2-bromoethyl)-5-ethyl-1,3-diazinane-2,4,6-trione · ligand · chains A, B, C, D, E
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D, E
- LMT · Dodecyl-beta-D-maltoside · additive · 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.87 | 0.91 | 84 | empty |
| 2 | 493 | 0.85 | 0.91 | 65 | empty |
| 3 | 441 | 0.85 | 0.92 | 53 | LMT, 6JW |
| 4 | 353 | 0.83 | 0.92 | 41 | empty |
| 5 | 332 | 0.82 | 0.92 | 39 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2317 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 2287 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 2271 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2257 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 2241 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5L4H · X-ray structure of the 2-22' locally-closed mutant of GLIC in complex with… · 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 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 5L4H · PDBe 5L4H · UniProt Q7NDN8
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