6R38

T. brucei FPPS in complex with 2-(2,5-dichlorobenzo[b]thiophen-3-yl)acetic acid

• PDB DOI: https://doi.org/10.2210/pdb6R38/pdb

• Classification: TRANSFERASE
• Organism(s): Trypanosoma brucei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-03-19 Released: 2020-04-08 
• Deposition Author(s): Muenzker, L., Petrick, J.K., Schleberger, C., Jahnke, W.
• Funding Organization(s): Marie Sklodowska-Curie Actions, FragNET ITN

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.249 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 

Starting Model: experimental

Literature

Targeting Trypanosoma brucei FPPS by Fragment-based drug discovery

Muenzker, L., Wolfgang, J.

(2019) Thesis 

• DOI: https://doi.org/10.17192/z2019.0500

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: 42.51 kDa 
• Atom Count: 2,663 
• Modelled Residue Count: 331 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl pyrophosphate synthase	A	369	Trypanosoma brucei	Mutation(s): 0
UniProt
Find proteins for Q86C09 (Trypanosoma brucei) Explore Q86C09  Go to UniProtKB:  Q86C09

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JQE	B [auth A]	2-[2,5-bis(chloranyl)-1-benzothiophen-3-yl]ethanoic acid C10 H6 Cl2 O2 S BCQFHYKPVHGTMB-UHFFFAOYSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.249 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.839	α = 90
b = 60.839	β = 90
c = 339.99	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-08 
Deposition Author(s): Muenzker, L., Petrick, J.K., Schleberger, C., Jahnke, W.

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Funding Organization	Location	Grant Number
Marie Sklodowska-Curie Actions, FragNET ITN	Switzerland	675899

Revision History  

• Version 1.0: 2020-04-08
  Type: Initial release
  
• Version 1.1: 2021-10-27
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Refinement description