Crystal structure of L. monocytogenes phosphodiesterase pgph hd domain in complex with cyclic-di-AMP

Structure

x-ray diffraction · 2 distinct chains · 70% helix, 1% strand (DSSP).

Ligands and binding sites

• 2BA · (2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-D:3', 2'-J][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5, 10,12-tetrol 5,12-dioxide · ligand · 2 copies · chains A, D
• FE · Fe (III) ion · metal · 4 copies · chains A, D

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

Pockets

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

Interfaces

1 interface between chains.

• A–D · 613 Ų buried · 7 hydrogen bonds · protein-protein

Compared structures

• 4S1B · Crystal Structure of L. monocytogenes phosphodiesterase PgpH HD domain in complex with… · 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 Q8Y746
• Elsewhere: RCSB PDB 4S1B · PDBe 4S1B · UniProt Q8Y746