Human phosphodiestrase-5'GMP complex (ep), produced by soaking with 20MM CGMP+20 mm MNCL2+20 mm MGCL2 for 2 hours, and flash-cooled to liquid nitrogen temperature when substrate was still abudant.

Structure

x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).

Ligands and binding sites

• 5GP · Guanosine-5'-monophosphate · ligand · chains A
• IBM · 3-isobutyl-1-methylxanthine · ligand · chains B
• MN · Manganese (II) ion · metal · 4 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B
• FMT · Formic acid · additive · chains 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, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 846 Ų buried · 12 hydrogen bonds · protein-protein

Compared structures

• 3DYS · human phosphodiestrase-5'GMP complex (EP), produced by soaking with 20mM cGMP+20 mM… · the same entry in another collection · chain A against A, TM-score 1.00
• O76083 · AlphaFold monomer V2.0 prediction for high affinity cgmp-specific 3',5'-cyclic… · a predicted model of the same protein · chain B against A, TM-score 0.99

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 O76083
• Elsewhere: RCSB PDB 3DYS · PDBe 3DYS · UniProt O76083