› 7qyh

X-ray diffraction
3.33Å resolution

Structure of plasmepsin II in complex with 2-aminoquinazolin-4(3H)-one based open-flap inhibitor

Released:
DOI: 10.2210/pdb7qyh/pdb
PDB entry 7qyh coloured by chain, front view.
PDB entry 7qyh coloured by chain, side view.
PDB entry 7qyh coloured by chain, top view.
Source organism: Plasmodium falciparum 3D7
Primary publication:
Exploring Aspartic Protease Inhibitor Binding to Design-Selective Antimalarials.
Bobrovs R, Basens EE, Drunka L, Kanepe I, Matisone S, Velins KK, Andrianov V, Leitis G, Zelencova-Gopejenko D, Rasina D, Jirgensons A, Jaudzems K
J Chem Inf Model (2022)
PMID: 35712895

Function and Biology Details

Reaction catalysed: 
Hydrolysis of the bonds linking certain hydrophobic residues in hemoglobin or globin. Also cleaves small molecules substrates such as Ala-Leu-Glu-Arg-Thr-Phe-|-Phe(NO(2))-Ser-Phe-Pro-Thr.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184717 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Plasmepsin II Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 329 amino acids
Theoretical weight: 36.91 KDa
Source organism: Plasmodium falciparum 3D7
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8I6V3 (Residues: 125-453; Coverage: 73%)
Gene names: PF3D7_1408000, PMII
Sequence domains: Eukaryotic aspartyl protease

Ligands and Environments

1 bound ligand:
Ligand I0J 1 x I0J
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: C2221
Unit cell:
a: 70.821Å b: 274.066Å c: 273.967Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.312 0.31 0.336
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 mention without citation

AlphaFold-SFA: Accelerated sampling of cryptic pocket opening, protein-ligand binding and allostery by AlphaFold, slow feature analysis and metadynamics.
Vats et al. (2024)