Plasmodium falciparum spermidine synthase in complex with 5'- methylthioadenosine and N,N'-BIS(3-aminopropyl)-1,4- cyclohexanediamine after catalysis in crystal

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 31% strand (DSSP).

Ligands and binding sites

• MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 3 copies · chains A, B, C
• GXQ · N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine · ligand · 2 copies · chains A, B
• 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · 2 copies · chains A, B, C
• JFQ · trans-N-(3-aminopropyl)cyclohexane-1,4-diamine · ligand · chains C
• GOL · Glycerol · additive · 7 copies · chains A, B, C

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

Pockets

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

Interfaces

2 interfaces between chains.

• B–C · 1507 Ų buried · 22 hydrogen bonds · protein-protein
• A–B · 486 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 6HY1 · Plasmodium falciparum spermidine synthase in complex with 5'-methylthioadenosine and… · 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 Q8II73
• Elsewhere: RCSB PDB 6HY1 · PDBe 6HY1 · UniProt Q8II73