› 5yic

X-ray diffraction
1.9Å resolution

Crystal Structure of KNI-10333 bound Plasmepsin II (PMII) from Plasmodium falciparum

Released:
DOI: 10.2210/pdb5yic/pdb
PDB entry 5yic coloured by chain, front view.
PDB entry 5yic coloured by chain, side view.
PDB entry 5yic coloured by chain, top view.
Source organism: Plasmodium falciparum 3D7
Primary publication:
Deciphering the mechanism of potent peptidomimetic inhibitors targeting plasmepsins - biochemical and structural insights.
Mishra V, Rathore I, Arekar A, Sthanam LK, Xiao H, Kiso Y, Sen S, Patankar S, Gustchina A, Hidaka K, Wlodawer A, Yada RY, Bhaumik P
FEBS J 285 3077-3096 (2018)
PMID: 29943906

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 Chain: A
Molecule details ›
Chain: A
Length: 328 amino acids
Theoretical weight: 36.86 KDa
Source organism: Plasmodium falciparum 3D7
Expression system: Enterobacteria phage L1
UniProt:
  • Canonical: Q8I6V3 (Residues: 126-453; Coverage: 72%)
Gene names: PF3D7_1408000, PMII
Sequence domains: Eukaryotic aspartyl protease
Structure domains: Acid Proteases

Ligands and Environments

3 bound ligands:
Ligand 8VO 1 x 8VO
Ligand CPS 1 x CPS
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: I4
Unit cell:
a: 106.5Å b: 106.5Å c: 71Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.178 0.227
Expression system: Enterobacteria phage L1

Quick links

Citations

1 review citation

Structural Insights Into Key Plasmodium Proteases as Therapeutic Drug Targets.
Mishra et al. (2019)
1 other article

1 mention without citation

Deciphering the mechanism of potent peptidomimetic inhibitors targeting plasmepsins - biochemical and structural insights.
Mishra et al. (2018)