1SME

PLASMEPSIN II, A HEMOGLOBIN-DEGRADING ENZYME FROM PLASMODIUM FALCIPARUM, IN COMPLEX WITH PEPSTATIN A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure and inhibition of plasmepsin II, a hemoglobin-degrading enzyme from Plasmodium falciparum.

Silva, A.M.Lee, A.Y.Gulnik, S.V.Maier, P.Collins, J.Bhat, T.N.Collins, P.J.Cachau, R.E.Luker, K.E.Gluzman, I.Y.Francis, S.E.Oksman, A.Goldberg, D.E.Erickson, J.W.

(1996) Proc.Natl.Acad.Sci.USA 93: 10034-10039


  • PubMed Abstract: 
  • Plasmodium falciparum is the major causative agent of malaria, a disease of worldwide importance. Resistance to current drugs such as chloroquine and mefloquine is spreading at an alarming rate, and our antimalarial armamentarium is almost depleted. ...

    Plasmodium falciparum is the major causative agent of malaria, a disease of worldwide importance. Resistance to current drugs such as chloroquine and mefloquine is spreading at an alarming rate, and our antimalarial armamentarium is almost depleted. The malarial parasite encodes two homologous aspartic proteases, plasmepsins I and II, which are essential components of its hemoglobin-degradation pathway and are novel targets for antimalarial drug development. We have determined the crystal structure of recombinant plasmepsin II complexed with pepstatin A. This represents the first reported crystal structure of a protein from P. falciparum. The crystals contain molecules in two different conformations, revealing a remarkable degree of interdomain flexibility of the enzyme. The structure was used to design a series of selective low molecular weight compounds that inhibit both plasmepsin II and the growth of P. falciparum in culture.


    Organizational Affiliation

    Structural Biochemistry Program, National Cancer Institute/SAIC, Frederick, MD 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PLASMEPSIN II
A, B
329Plasmodium falciparumEC: 3.4.23.39
Find proteins for P46925 (Plasmodium falciparum)
Go to UniProtKB:  P46925
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pepstatin
C, D
6N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000557
Query on PRD_000557
C,DPepstatinOligopeptide / Enzyme inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IHNKi: 0.006 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.195 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.100α = 90.00
b = 142.100β = 90.00
c = 97.600γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-01-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2013-02-27
    Type: Other