Agao in complex with WC4D3 (ru-wire inhibitor, 4-carbon linker, delta enantiomer, data set 3)

Structure

x-ray diffraction · 1 distinct chain · 13% helix, 43% strand (DSSP).

Ligands and binding sites

• R4A · Bis[1h,1'h-2,2'-bipyridinato(2-)-kappa~2~n~1~,n~1'~]{3-[4-(1,10-dihydro-1,10-phenanthrolin-4-yl-kappa~2~n~1~,n~10~)butoxy]-N,N-dimethylanilinato(2-)}ruthenium · ligand · 2 copies · chains A, B
• CU · Copper (II) ion · metal · 2 copies · chains A, B
• NA · Sodium ion · metal · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 2 copies · chains A, B
• GOL · Glycerol · additive · 11 copies · chains A, B

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

Pockets

15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 6822 Ų buried · 106 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 2 modified, 1 covalent (disulfide, nonstandard, covalent ligand).

Compared structures

• 2CFG · AGAO in complex with wc4d3 (Ru-wire inhibitor, 4-carbon linker, delta enantiomer, data… · 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 P46881
• Elsewhere: RCSB PDB 2CFG · PDBe 2CFG · UniProt P46881