Cryo-EM of the SLFN12-PDE3A complex: PDE3A body refinement

Structure

electron microscopy · 2 distinct chains · 63% helix, 3% strand (DSSP).

Ligands and binding sites

• X5M · (4~{R})-3-[4-(diethylamino)-3-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]-4-methyl-4,5-dihydro-1~{H}-pyridazin-6-one · ligand · 2 copies · chains B, A, C, D
• MN · Manganese (II) ion · metal · 2 copies · chains B, C
• MG · Magnesium ion · metal · 2 copies · chains B, C

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

Pockets

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

Interfaces

3 interfaces between chains.

• B–C · 881 Ų buried · 12 hydrogen bonds · protein-protein
• C–D · 543 Ų buried · 1 hydrogen bond · protein-protein
• B–A · 541 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 7LRC · Cryo-EM of the SLFN12-PDE3A complex: PDE3A body refinement · the same entry in another collection · chain B against B, TM-score 1.00
• Q14432 · AlphaFold monomer V2.0 prediction for cgmp-inhibited 3',5'-cyclic phosphodiesterase a… · a predicted model of the same protein · chain B against A, TM-score 0.99
• Q8IYM2 · AlphaFold monomer V2.0 prediction for schlafen family member 12 (Q8IYM2) · a predicted model of the same protein · chain A against A, TM-score 0.80

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 Q14432
• Every structure of UniProt Q8IYM2
• Elsewhere: RCSB PDB 7LRC · PDBe 7LRC · UniProt Q14432 · UniProt Q8IYM2