6SI5 | pdb_00006si5

T. cruzi FPPS in complex with 1-methyl-5-(4,5,6,7-tetrahydrothieno[3,2-c]pyridine-5-carbonyl)pyridin-2(1H)-one

• PDB DOI: https://doi.org/10.2210/pdb6SI5/pdb

• Classification: TRANSFERASE
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-08-08 Released: 2020-08-26 
• Deposition Author(s): Petrick, J.K., Muenzker, L., Schleberger, C., Cornaciu, I., Clavel, D., Marquez, J.A., Jahnke, W.
• Funding Organization(s): European Commission, Accelerated Early staGe drug dIScovery

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.260 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Targeting farnesyl pyrophosphate synthase of Trypanosoma cruzi by fragment-based lead discovery

Petrick, J.K., Jahnke, W.

(2019) Thesis 

• DOI: https://doi.org/10.17192/z2019.0501

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.83 kDa 
• Atom Count: 2,997 
• Modeled Residue Count: 354 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl diphosphate synthase	A	364	Trypanosoma cruzi	Mutation(s): 0
UniProt
Find proteins for Q8WS26 (Trypanosoma cruzi) Explore Q8WS26  Go to UniProtKB:  Q8WS26

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LEQ (Subject of Investigation/LOI)	B [auth A]	5-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylcarbonyl)-1-methyl-pyridin-2-one C14 H14 N2 O2 S PXCRFQLKGNEWBG-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.260 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.061	α = 90
b = 58.061	β = 90
c = 396.793	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Petrick, J.K., Muenzker, L., Schleberger, C., Cornaciu, I., Clavel, D., Marquez, J.A., Jahnke, W.

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Funding Organization	Location	Grant Number
European Commission		765555
Accelerated Early staGe drug dIScovery		765555

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2023-03-01
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description