3RIE

The structure of Plasmodium falciparum spermidine synthase in complex with 5'-methylthioadenosine and N-(3-aminopropyl)-trans-cyclohexane-1,4-diamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

A novel inhibitor of Plasmodium falciparum spermidine synthase: a twist in the tail.

Burger, P.B.Williams, M.Sprenger, J.Reeksting, S.B.Botha, M.Muller, I.B.Joubert, F.Birkholtz, L.M.Louw, A.I.

(2015) Malar J 14: 54-54

  • DOI: 10.1186/s12936-015-0572-z

  • PubMed Abstract: 
  • Plasmodium falciparum is the most pathogenic of the human malaria parasite species and a major cause of death in Africa. It's resistance to most of the current drugs accentuates the pressing need for new chemotherapies. Polyamine metabolism of the pa ...

    Plasmodium falciparum is the most pathogenic of the human malaria parasite species and a major cause of death in Africa. It's resistance to most of the current drugs accentuates the pressing need for new chemotherapies. Polyamine metabolism of the parasite is distinct from the human pathway making it an attractive target for chemotherapeutic development. Plasmodium falciparum spermidine synthase (PfSpdS) catalyzes the synthesis of spermidine and spermine. It is a major polyamine flux-determining enzyme and spermidine is a prerequisite for the post-translational activation of P. falciparum eukaryotic translation initiation factor 5A (elF5A). The most potent inhibitors of eukaryotic SpdS's are not specific for PfSpdS.


    Organizational Affiliation

    Department of Biochemistry, UP Centre for Sustainable Malaria Control, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa. pieter.burger@gmail.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spermidine synthase
A, B, C
283Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 2.5.1.16
Find proteins for Q8II73 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8II73
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JFQ
Query on JFQ

Download SDF File 
Download CCD File 
A, B, C
trans-N-(3-aminopropyl)cyclohexane-1,4-diamine
C9 H21 N3
QIMPCSMJRMPRJC-KYZUINATSA-N
 Ligand Interaction
1PG
Query on 1PG

Download SDF File 
Download CCD File 
C
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
C11 H24 O6
SLNYBUIEAMRFSZ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MTA
Query on MTA

Download SDF File 
Download CCD File 
A, B, C
5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 196.800α = 90.00
b = 134.590β = 94.55
c = 48.460γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
XSCALEdata scaling
CNSphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references
  • Version 1.2: 2018-03-07
    Type: Advisory, Data collection
  • Version 1.3: 2019-07-17
    Type: Data collection, Refinement description
  • Version 1.4: 2019-09-04
    Type: Advisory, Data collection