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

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.271 

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This is version 1.6 of the entry. See complete history


Recombinant plasmepsin 1 from the human malaria parasite plasmodium falciparum: enzymatic characterization, active site inhibitor design, and structural analysis.

Liu, P.Marzahn, M.R.Robbins, A.H.Gutierrez-de-Teran, H.Rodriguez, D.McClung, S.H.Stevens, S.M.Yowell, C.A.Dame, J.B.McKenna, R.Dunn, B.M.

(2009) Biochemistry 48: 4086-4099

  • DOI: https://doi.org/10.1021/bi802059r
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A mutated form of truncated proplasmepsin 1 (proPfPM1) from the human malaria parasite Plasmodium falciparum, proPfPM1 K110pN, was generated and overexpressed in Escherichia coli. The automaturation process was carried out at pH 4.0 and 4.5, and the optimal catalytic pH of the resulting mature PfPM1 was determined to be pH 5.5. This mature PfPM1 showed comparable binding affinity to peptide substrates and inhibitors with the naturally occurring form isolated from parasites. The S3-S3' subsite preferences of the recombinant mature PfPM1 were explored using combinatorial chemistry based peptide libraries. On the basis of the results, a peptidomimetic inhibitor (compound 1) was designed and yielded 5-fold selectivity for binding to PfPM1 versus the homologous human cathepsin D (hcatD). The 2.8 A structure of the PfPM2-compound 1 complex is reported. Modeling studies were conducted using a series of peptidomimetic inhibitors (compounds 1-6, Table 3) and three plasmepsins: the crystal structure of PfPM2, and homology derived models of PfPM1 and PfPM4.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida 32610-0245, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C [auth B]
329Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: plasmepsin 2
Find proteins for P46925 (Plasmodium falciparum (isolate HB3))
Explore P46925 
Go to UniProtKB:  P46925
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46925
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
peptide-based inhibitorB [auth C],
8N/AMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.271 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 219.489α = 90
b = 69.032β = 102.85
c = 53.578γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2011-08-17
    Changes: Non-polymer description
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2017-10-25
    Changes: Refinement description
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2023-11-15
    Changes: Data collection