Crystal structure of human glycine receptor alpha-3 mutant N38Q bound to am-3607

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 30% strand (DSSP).

Ligands and binding sites

• 7C6 · (3s,3as,9bs)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3A,5,9B-hexahydro-4H-pyrrolo[3,4-C][1, 6]naphthyridin-4-one · ligand · 5 copies · chains A, B, C, D, E
• GLY · Glycine · ligand · 5 copies · chains A, B, C, D, E
• ZN · Zinc ion · metal · 5 copies · chains A, B, C, D, E
• CL · Chloride ion · ion

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–B · 2389 Ų buried · 19 hydrogen bonds · protein-protein
• C–D · 2384 Ų buried · 21 hydrogen bonds · protein-protein
• B–C · 2375 Ų buried · 22 hydrogen bonds · protein-protein
• D–E · 2366 Ų buried · 18 hydrogen bonds · protein-protein
• A–E · 2337 Ų buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

• 5TIN · Crystal Structure of Human Glycine Receptor alpha-3 Mutant N38Q Bound to AM-3607 · the same entry in another collection · chain E against E, TM-score 1.00
• O75311 · AlphaFold monomer V2.0 prediction for glycine receptor subunit alpha-3 (O75311) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O75311
• Elsewhere: RCSB PDB 5TIN · PDBe 5TIN · UniProt O75311