1SME | pdb_00001sme

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 
    0.195 (Depositor) 
  • R-Value Observed: 
    0.195 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 2.1 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 U S A 93: 10034-10039

  • DOI: https://doi.org/10.1073/pnas.93.19.10034
  • Primary Citation Related Structures: 
    1SME

  • 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. 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.

Macromolecule Content 

  • Total Structure Weight: 75.28 kDa 
  • Atom Count: 5,425 
  • Modeled Residue Count: 670 
  • Deposited Residue Count: 670 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PLASMEPSIN II
A, B
329Plasmodium falciparumMutation(s): 0 
EC: 3.4.23.39
UniProt
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
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Pepstatin
C, D
6Streptomyces argenteolus subsp. toyonakensisMutation(s): 0 

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work:  0.195 (Depositor) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.1α = 90
b = 142.1β = 90
c = 97.6γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-01-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2013-02-27
    Changes: Other
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2024-10-23
    Changes: Structure summary