3OZA

Crystal Structure of Plasmodium falciparum 3-Phosphoglycerate Kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of Plasmodium falciparum phosphoglycerate kinase: Evidence for anion binding in the basic patch.

Smith, C.D.Chattopadhyay, D.Pal, B.

(2011) Biochem.Biophys.Res.Commun. 412: 203-206

  • DOI: 10.1016/j.bbrc.2011.07.045
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 3-Phosphoglycerate kinase (EC 2.7.2.3) is a key enzyme in the glycolytic pathway and catalyzes an important phosphorylation step leading to the production of ATP. The crystal structure of Plasmodium falciparum phosphoglycerate kinase (PfPGK) in the o ...

    3-Phosphoglycerate kinase (EC 2.7.2.3) is a key enzyme in the glycolytic pathway and catalyzes an important phosphorylation step leading to the production of ATP. The crystal structure of Plasmodium falciparum phosphoglycerate kinase (PfPGK) in the open conformation is presented in two different groups, namely I222 and P6(1)22. The structure in I222 space group is solved using MAD and refined at 3Å whereas that in P6(1)22A is solved using MR and refined at 2.7Å. I222 form has three monomers in asymmetric unit whereas P6(1)22 form has two monomers in the asymmetric unit. In both crystal forms a sulphate ion is located at the active site where ATP binds, but no Mg(2+) ion is observed. For the first time another sulphate ion is found at the basic patch where the 3-phosphate of 1,3-biphosphoglycerate normally binds. This was found in both chains of P6(1)22 form but only in chain A of I222 form.


    Organizational Affiliation

    University of Alabama at Birmingham, Birmingham, AL 35294, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoglycerate kinase
A, B, C
424Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
Gene Names: PGK
EC: 2.7.2.3
Find proteins for P27362 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  P27362
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.200 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 119.030α = 90.00
b = 147.610β = 90.00
c = 206.490γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SOLVEphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2011-09-14
    Type: Database references