A novel interaction mode between a microbial ggdef domain and the bis- (3, 5 )-cyclic di-gmp

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 21% strand (DSSP).

Ligands and binding sites

• C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B
• PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 355 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 3QYY · A Novel Interaction Mode between a Microbial GGDEF Domain and the Bis-(3, 5 )-cyclic… · 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 Q8P559
• Elsewhere: RCSB PDB 3QYY · PDBe 3QYY · UniProt Q8P559