3KTX

Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK)in complex with 1,3,6,8-pyrenetetrasulfonic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

An improved strategy for the crystallization of Leishmania mexicana pyruvate kinase.

Morgan, H.P.McNae, I.W.Hsin, K.Y.Michels, P.A.Fothergill-Gilmore, L.A.Walkinshaw, M.D.

(2010) Acta Crystallogr.,Sect.F 66: 215-218

  • DOI: 10.1107/S1744309109053494
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The inclusion of novel small molecules in crystallization experiments has provided very encouraging results and this method is now emerging as a promising alternative strategy for crystallizing 'problematic' biological macromolecules. These small mol ...

    The inclusion of novel small molecules in crystallization experiments has provided very encouraging results and this method is now emerging as a promising alternative strategy for crystallizing 'problematic' biological macromolecules. These small molecules have the ability to promote lattice formation through stabilizing intermolecular interactions in protein crystals. Here, the use of 1,3,6,8-pyrenetetrasulfonic acid (PTS), which provides a helpful intermolecular bridge between Leishmania mexicana PYK (LmPYK) macromolecules in the crystal, is reported, resulting in the rapid formation of a more stable crystal lattice at neutral pH and greatly improved X-ray diffraction results. The refined structure of the LmPYK-PTS complex revealed the negatively charged PTS molecule to be stacked between positively charged (surface-exposed) arginine side chains from neighbouring LmPYK molecules in the crystal lattice.


    Organizational Affiliation

    Structural Biochemistry Group, Institute of Structural and Molecular Biology, The University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate kinase
A, B
499Leishmania mexicanaMutation(s): 0 
Gene Names: PYK
EC: 2.7.1.40
Find proteins for Q27686 (Leishmania mexicana)
Go to UniProtKB:  Q27686
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PTK
Query on PTK

Download SDF File 
Download CCD File 
A
pyrene-1,3,6,8-tetrasulfonic acid
1,3,6,8-pyrenetetrasulfonic acid
C16 H10 O12 S4
CZLSHVQVNDDHDQ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.186 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 122.860α = 90.00
b = 129.860β = 90.00
c = 165.200γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
PHASERphasing
SCALAdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-28
    Type: Database references