Crystal structure of the ternary complex of gephe-ADP-GABA(A) receptor derived peptide

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 33% strand (DSSP).

Ligands and binding sites

• ADP · Adenosine-5'-diphosphate · ligand · chains A
• 3F8 · 1,1'-[ethane-1,2-diylbis(oxyethane-2,1-diyl)]bis(1H-pyrrole-2,5-dione) · ligand · chains D, E
• MG · Magnesium ion · metal · 2 copies · chains A
• NA · Sodium ion · metal · chains A
• PO4 · Phosphate ion · ion · chains A
• ACT · Acetate ion · additive · 8 copies · chains A
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

2 interfaces between chains.

• A–D · 628 Ų buried · 4 hydrogen bonds · protein-protein
• D–E · 13 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 6HSN · Crystal structure of the ternary complex of GephE-ADP-GABA(A) receptor derived peptide · the same entry in another collection · chain A against A, TM-score 1.00
• Q03555 · AlphaFold monomer V2.0 prediction for gephyrin (Q03555) · a predicted model of the same protein · chain A against A, TM-score 0.98
• P20236 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor subunit alpha-3… · a predicted model of the same protein · chain D against A, TM-score 0.41

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 Q03555
• Every structure of UniProt P20236
• Elsewhere: RCSB PDB 6HSN · PDBe 6HSN · UniProt Q03555 · UniProt P20236