› 4y6m

X-ray diffraction
2.27Å resolution

Structure of plasmepsin II from Plasmodium falciparum complexed with inhibitor PG418

Released:
DOI: 10.2210/pdb4y6m/pdb
PDB entry 4y6m coloured by chain, front view.
PDB entry 4y6m coloured by chain, side view.
PDB entry 4y6m coloured by chain, top view.
Source organism: Plasmodium falciparum
Primary publication:
Structures of plasmepsin II from Plasmodium falciparum in complex with two hydroxyethylamine-based inhibitors.
Recacha R, Leitans J, Akopjana I, Aprupe L, Trapencieris P, Jaudzems K, Jirgensons A, Tars K
Acta Crystallogr F Struct Biol Commun 71 1531-9 (2015)
PMID: 26625296

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-155535 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Plasmepsin II Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 329 amino acids
Theoretical weight: 36.95 KDa
Source organism: Plasmodium falciparum
Expression system: Escherichia coli
UniProt:
  • Canonical: P46925 (Residues: 125-453; Coverage: 73%)
Gene name: PMII
Sequence domains: Eukaryotic aspartyl protease
Structure domains: Acid Proteases

Ligands and Environments

2 bound ligands:
Ligand 48Q 3 x 48Q
Ligand GOL 6 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I711
Spacegroup: P212121
Unit cell:
a: 81.22Å b: 104.6Å c: 111.68Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.172 0.219
Expression system: Escherichia coli

Quick links

Citations

7 citation in other articles

A multistage antimalarial targets the plasmepsins IX and X essential for invasion and egress.
Pino et al. (2017)
6 more

3 mentions without citation

Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments.
Bhakat S. (2021)
2 more