Crystal structure of a dinucleotide-binding protein (Y224A) of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (form II)

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).

Ligands and binding sites

• FGO · [(1s,3r,3ar,6as)-3-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-5,5-bis(oxidanyl)-1,3,3A,4,6,6A-hexahydrocyclopenta[c]furan-1-yl]methyl [(2R,3S,4R, 5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate · ligand · 2 copies · chains A, B
• NA · Sodium ion · metal · chains A
• CO2 · Carbon dioxide · ion · 2 copies · chains A, B
• GOL · Glycerol · additive · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 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, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 305 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 7C0W · Crystal structure of a dinucleotide-binding protein (Y224A) of ABC transporter… · 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 Q5SLB4
• Elsewhere: RCSB PDB 7C0W · PDBe 7C0W · UniProt Q5SLB4