Crystal structure of the eal domain of C-di-gmp specific phosphodiesterase yaha in complex with substrate C-di-gmp and ca++

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 25% 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
• HB0 · trans-4-(hydroxymethyl)cyclohexanol · ligand · 2 copies · chains A, B
• CA · Calcium ion · metal · 4 copies · chains A, B
• IMD · Imidazole · additive · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1448 Ų buried · 32 hydrogen bonds · protein-protein

Compared structures

• 4LJ3 · Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in… · the same entry in another collection · chain A against A, TM-score 1.00
• P21514 · AlphaFold monomer V2.0 prediction for cyclic di-gmp phosphodiesterase pdel (P21514) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P21514
• Elsewhere: RCSB PDB 4LJ3 · PDBe 4LJ3 · UniProt P21514