› 2r9b

X-ray diffraction
2.8Å resolution

Structural Analysis of Plasmepsin 2 from Plasmodium falciparum complexed with a peptide-based inhibitor

Released:
DOI: 10.2210/pdb2r9b/pdb
PDB entry 2r9b coloured by chain, front view.
PDB entry 2r9b coloured by chain, side view.
PDB entry 2r9b coloured by chain, top view.
Source organism: Plasmodium falciparum 3D7
Primary publication:
Recombinant plasmepsin 1 from the human malaria parasite plasmodium falciparum: enzymatic characterization, active site inhibitor design, and structural analysis.
Liu P, Marzahn MR, Robbins AH, Gutiérrez-de-Terán H, Rodríguez D, McClung SH, Stevens SM, Yowell CA, Dame JB, McKenna R, Dunn BM
Biochemistry 48 4086-99 (2009)
PMID: 19271776

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 domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155539 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Plasmepsin II Chains: A, B
Molecule details ›
Chains: A, B
Length: 329 amino acids
Theoretical weight: 36.95 KDa
Source organism: Plasmodium falciparum 3D7
Expression system: Escherichia coli
UniProt:
  • Canonical: P46925 (Residues: 125-453; Coverage: 73%)
Gene name: PMII
Sequence domains: Eukaryotic aspartyl protease
Structure domains: Acid Proteases
peptide-based inhibitor Chains: C, D
Molecule details ›
Chains: C, D
Length: 8 amino acids
Theoretical weight: 966 Da
Source organism: Plasmodium falciparum 3D7
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: C2
Unit cell:
a: 219.489Å b: 69.032Å c: 53.578Å
α: 90° β: 102.85° γ: 90°
R-values:
R R work R free
0.286 0.238 0.286
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Malaria parasite plasmepsins: More than just plain old degradative pepsins.
Nasamu et al. (2020)
1 more

4 mentions without citation

Structural studies of vacuolar plasmepsins.
Bhaumik et al. (2012)
3 more