1LF2

CRYSTAL STRUCTURE OF PLASMEPSIN II FROM P FALCIPARUM IN COMPLEX WITH INHIBITOR RS370


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of Ser205 mutant plasmepsin II from Plasmodium falciparum at 1.8 A in complex with the inhibitors rs367 and rs370.

Asojo, O.A.Afonina, E.Gulnik, S.V.Yu, B.Erickson, J.W.Randad, R.Medjahed, D.Silva, A.M.

(2002) Acta Crystallogr.,Sect.D 58: 2001-2008

  • Primary Citation of Related Structures:  1LEE

  • PubMed Abstract: 
  • Plasmepsin II is one of the four catalytically active plasmepsins found in the food vacuole of Plasmodium falciparum. These enzymes initiate hemoglobin degradation by cleavage at the alpha-chain between Phe33 and Leu34. The crystal structures of Ser2 ...

    Plasmepsin II is one of the four catalytically active plasmepsins found in the food vacuole of Plasmodium falciparum. These enzymes initiate hemoglobin degradation by cleavage at the alpha-chain between Phe33 and Leu34. The crystal structures of Ser205 mutant plasmepsin II from P. falciparum in complex with two inhibitors have been refined at a resolution of 1.8 A in the space group I222 and to R factors of 19.9 and 19.5%. Each crystal contains one monomer in the asymmetric unit. Both inhibitors have a Phe-Leu core and incorporate tetrahedral transition-state mimetic hydroxypropylamine. The inhibitor rs367 possesses a 2,6-dimethylphenyloxyacetyl group at the P2 position and 3-aminobenzamide at the P2' position, while rs370 has the same P2 group but 4-aminobenzamide in the P2' position. These complexes reveal key conserved hydrogen bonds between the inhibitor and the binding-cavity residues, notably with the flap residues Val78 and Ser79, the catalytic dyad Asp34 and Asp214 and the residues Ser218 and Gly36 that are in proximity to the catalytic dyad. The structures also show unexpected conformational variability of the binding cavity of plasmepsin II and may reflect the mode of binding of the hemoglobin alpha-chain for cleavage.


    Related Citations: 
    • Novel uncomplexed and complexed structures of plasmepsin II, an aspartic protease from Plasmodium falciparum.
      Asojo, O.A.,Gulnik, S.V.,Afonina, E.,Yu, B.,Ellman, J.A.,Haque, T.S.,Silva, A.M.
      (2003) J.Mol.Biol. 327: 173


    Organizational Affiliation

    Structure Biochemistry Program, National Cancer Institute/SAIC, Frederick, MD 21702, USA. asojo@ncifcrf.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plasmepsin 2
A
331Plasmodium falciparumEC: 3.4.23.39
Find proteins for P46925 (Plasmodium falciparum)
Go to UniProtKB:  P46925
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R37
Query on R37

Download SDF File 
Download CCD File 
A
3-AMINO-N-{4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-1-ISOBUTYL-5-PHENYL-PENTYL}-BENZAMIDE
C32 H41 N3 O4
APJAEXGNDLFGPD-AWCRTANDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
R37Ki: 30 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.195 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 75.890α = 90.00
b = 84.830β = 90.00
c = 123.080γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-10
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance