Crystal structure of the G20A mutant C-di-gmp riboswith bound to C-di- gmp

Structure

x-ray diffraction · 2 distinct chains · 28% 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 · chains R
• MG · Magnesium ion · metal · 2 copies · chains R

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

Pockets

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

Interfaces

1 interface between chains.

• P–R · 995 Ų buried · 27 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

• 3MUM · Crystal Structure of the G20A mutant c-di-GMP riboswith bound to c-di-GMP · the same entry in another collection · chain P against P, TM-score 1.00
• P09012 · AlphaFold monomer V2.0 prediction for U1 small nuclear ribonucleoprotein a (P09012) · a predicted model of the same protein · chain P against A, TM-score 0.95

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 P09012
• Elsewhere: RCSB PDB 3MUM · PDBe 3MUM · UniProt P09012