X-ray structure of the 2-22' locally-closed mutant of glic in complex with cyanoselenobarbital (seleniated barbiturate)

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 34% strand (DSSP).

Ligands and binding sites

• 6JA · 2-[5-ethyl-2,4,6-tris(oxidanylidene)-1,3-diazinan-5-yl]ethyl selenocyanate · ligand · chains A, B, C, D, E
• D12 · Dodecane · ligand · chains A, B, C, D, E
• NA · Sodium ion · metal · 4 copies · chains A, C, D, E
• CL · Chloride ion · ion · 5 copies · chains A, B, C, D, E
• ACT · Acetate ion · additive · 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.

Interfaces

5 interfaces between chains.

• A–E · 2349 Ų buried · 22 hydrogen bonds · protein-protein
• B–C · 2344 Ų buried · 16 hydrogen bonds · protein-protein
• D–E · 2337 Ų buried · 19 hydrogen bonds · protein-protein
• A–B · 2333 Ų buried · 20 hydrogen bonds · protein-protein
• C–D · 2303 Ų buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

• 5L47 · 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 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 5L47 · PDBe 5L47 · UniProt Q7NDN8