Crystal structure of kni-10395 bound histo-aspartic protease (hap) from plasmodium falciparum

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 46% strand (DSSP).

Ligands and binding sites

• K95 · (4R)-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-3-[(2S,3S)-2-hydroxy-3-{[S-methyl-N-(phenylacetyl)-L-cysteinyl]ami no}-4-phenylbutanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide · ligand · 3 copies · chains A, B, C, D
• NA · Sodium ion · metal · chains B, D
• EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C, D
• PG4 · Tetraethylene glycol · additive · 4 copies · chains A, B, D
• ACT · Acetate ion · additive · chains A
• PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · chains A, B

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

Pockets

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

Interfaces

6 interfaces between chains.

• A–B · 3957 Ų buried · 36 hydrogen bonds · protein-protein
• C–D · 3923 Ų buried · 32 hydrogen bonds · protein-protein
• B–D · 951 Ų buried · 16 hydrogen bonds · protein-protein
• A–C · 141 Ų buried · 2 hydrogen bonds · protein-protein
• A–D · 84 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

• 3QVI · Crystal structure of KNI-10395 bound histo-aspartic protease (HAP) from Plasmodium… · 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 Q9Y006
• Elsewhere: RCSB PDB 3QVI · PDBe 3QVI · UniProt Q9Y006