3SRK

A new class of suicide inhibitor blocks nucleotide binding to pyruvate kinase

• PDB DOI: https://doi.org/10.2210/pdb3SRK/pdb

• Classification: Transferase/Inhibitor
• Organism(s): Leishmania mexicana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-07-07 Released: 2012-07-18 
• Deposition Author(s): Morgan, H.P., Walsh, M., Blackburn, E.A., Wear, M.A., Boxer, M., Shen, M., McNae, I.W., Michels, P.A.M., Auld, D.S., Fothergill-Gilmore, L.A., Walkinshaw, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.266 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 

Literature

A new class of suicide inhibitor blocks nucleotide binding to pyruvate kinase

Morgan, H.P., Walsh, M., Blackburn, E.A., Wear, M.A., Boxer, M., Shen, M., McNae, I.W., Michels, P.A.M., Auld, D.S., Fothergill-Gilmore, L.A., Walkinshaw, M.D.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 109.98 kDa 
• Atom Count: 7,061 
• Modelled Residue Count: 898 
• Deposited Residue Count: 998 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase	A, B	499	Leishmania mexicana	Mutation(s): 0  Gene Names: PYK EC: 2.7.1.40
UniProt
Find proteins for Q27686 (Leishmania mexicana) Explore Q27686  Go to UniProtKB:  Q27686

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PTK	F [auth A]	pyrene-1,3,6,8-tetrasulfonic acid C16 H10 O12 S4 CZLSHVQVNDDHDQ-UHFFFAOYSA-N
LSA	C [auth A], G [auth B]	1,2-BENZISOTHIAZOL-3(2H)-ONE 1,1-DIOXIDE C7 H5 N O3 S CVHZOJJKTDOEJC-UHFFFAOYSA-N
K	D [auth A], E [auth A], H [auth B], I [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.266 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.42	α = 90
b = 130.16	β = 90
c = 166.49	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-18 
Deposition Author(s): Morgan, H.P., Walsh, M., Blackburn, E.A., Wear, M.A., Boxer, M., Shen, M., McNae, I.W., Michels, P.A.M., Auld, D.S., Fothergill-Gilmore, L.A., Walkinshaw, M.D.

Revision History  

• Version 1.0: 2012-07-18
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary