4C81

IspF (Plasmodium falciparum) CDP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structures of Ispf from Plasmodium Falciparum and Burkholderia Cenocepacia: Comparisons Inform Antimicrobial Drug Target Assessment.

O Rourke, P.E.Kalinowska-Tluscik, J.Fyfe, P.K.Dawson, A.Hunter, W.N.

(2014) Bmc Struct.Biol. 14: 1

  • DOI: 10.1186/1472-6807-14-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF) catalyzes the conversion of 4-diphosphocytidyl-2C-methyl-D-erythritol-2-phosphate to 2C-methyl-D-erythritol-2,4-cyclodiphosphate and cytidine monophosphate in production of isoprenoid-precur ...

    2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF) catalyzes the conversion of 4-diphosphocytidyl-2C-methyl-D-erythritol-2-phosphate to 2C-methyl-D-erythritol-2,4-cyclodiphosphate and cytidine monophosphate in production of isoprenoid-precursors via the methylerythritol phosphate biosynthetic pathway. IspF is found in the protozoan Plasmodium falciparum, a parasite that causes cerebral malaria, as well as in many Gram-negative bacteria such as Burkholderia cenocepacia. IspF represents a potential target for development of broad-spectrum antimicrobial drugs since it is proven or inferred as essential in these pathogens and absent from mammals. Structural studies of IspF from these two important yet distinct pathogens, and comparisons with orthologues have been carried out to generate reagents, to support and inform a structure-based approach to early stage drug discovery.


    Organizational Affiliation

    Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK. w.n.hunter@dundee.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
A
184Plasmodium falciparum (isolate 3D7)Mutation(s): 1 
Gene Names: ISPF
EC: 4.6.1.12
Find proteins for P62368 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  P62368
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CDP
Query on CDP

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Download CCD File 
A
CYTIDINE-5'-DIPHOSPHATE
C9 H15 N3 O11 P2
ZWIADYZPOWUWEW-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.144 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 84.864α = 90.00
b = 84.864β = 90.00
c = 101.031γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-08
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Database references