6R08 | pdb_00006r08

T. cruzi FPPS in complex with 3-(carboxymethyl)-5,7-dichloro-1H-indole-2-carboxylic acid

• PDB DOI: https://doi.org/10.2210/pdb6R08/pdb

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


• Deposited: 2019-03-12 Released: 2020-04-01 
• Deposition Author(s): Petrick, J.K., Muenzker, L., Schleberger, C., Jahnke, W.
• Funding Organization(s): Accelerated Early staGe drug dIScovery (AEGIS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 
  0.213 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (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 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.87 kDa 
• Atom Count: 3,320 
• Modeled Residue Count: 360 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GO1 (Subject of Investigation/LOI)	B [auth A]	3-(carboxymethyl)-5,7-dichloro-1H-indole-2-carboxylic acid C11 H7 Cl2 N O4 UDTYSEWCICAFSB-UHFFFAOYSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free:  0.213 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.895	α = 90
b = 57.895	β = 90
c = 398.225	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-01 
Deposition Author(s): Petrick, J.K., Muenzker, L., Schleberger, C., Jahnke, W.

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Funding Organization	Location	Grant Number
Accelerated Early staGe drug dIScovery (AEGIS)		765555

Revision History  

• Version 1.0: 2020-04-01
  Type: Initial release
  
• Version 1.1: 2023-03-01
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description