Crystal structure of glycine binding protein in complex with bicuculline

Structure

x-ray diffraction · 5 distinct chains · 9% helix, 50% strand (DSSP).

Ligands and binding sites

• J94 · (5S)-6,6-dimethyl-5-[(6R)-8-oxo-6,8-dihydrofuro[3,4-e][1,3]benzodioxol-6-yl]-5,6,7,8-tetrahydro[1, 3]dioxolo[4,5-g]isoquinolin-6-ium · ligand · 5 copies · chains A, B, C, D, E
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, 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

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• D–E · 1366 Ų buried · 14 hydrogen bonds · protein-protein
• A–B · 1314 Ų buried · 17 hydrogen bonds · protein-protein
• B–C · 1305 Ų buried · 14 hydrogen bonds · protein-protein
• A–E · 1283 Ų buried · 14 hydrogen bonds · protein-protein
• C–D · 1204 Ų buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

• 5OBH · Crystal structure of glycine binding protein in complex with bicuculline · the same entry in another collection · chain A 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 Q8WSF8
• Elsewhere: RCSB PDB 5OBH · PDBe 5OBH · UniProt Q8WSF8