Crystal structure of vibrio cholerae dncv cyclic AMP-gmp synthase in complex with linear intermediate 5' PPPA(3',5')PG

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 13% strand (DSSP).

Ligands and binding sites

• 38V · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3-[[(2R,3S,4R,5R)-5-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]methoxy-[[oxidanyl(phosphonooxy)phosphoryl]methyl]phosphinic acid · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · 4 copies · chains A, B
• ACT · Acetate ion · additive · 3 copies · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 562 Ų buried · 8 hydrogen bonds · protein-protein

Compared structures

• 4TY0 · Crystal structure of Vibrio cholerae DncV cyclic AMP-GMP synthase in complex with linear… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9KVG7 · AlphaFold monomer V2.0 prediction for cyclic gmp-AMP synthase (Q9KVG7) · a predicted model of the same protein · chain B 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 Q9KVG7
• Elsewhere: RCSB PDB 4TY0 · PDBe 4TY0 · UniProt Q9KVG7