6SII | pdb_00006sii

T. brucei FPPS in complex with 1-((1H-indol-3-yl)methyl)-N-(3-chlorobenzyl)piperidin-4-amine

• PDB DOI: https://doi.org/10.2210/pdb6SII/pdb

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


• Deposited: 2019-08-09 Released: 2020-08-26 
• Deposition Author(s): Muenzker, L., Petrick, J.K., Schleberger, C., Jahnke, W.
• Funding Organization(s): Other government, Marie Sklodowska-Curie Actions, FragNET ITN

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.276 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Starting Model: experimental

Literature

T. brucei FPPS

Muenzker, L., Jahnke, W.

To be published.

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: 42.62 kDa 
• Atom Count: 2,650 
• Modeled Residue Count: 328 
• 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
LEZ (Subject of Investigation/LOI)	B [auth A]	~{N}-[(3-chlorophenyl)methyl]-1-(1~{H}-indol-3-ylmethyl)piperidin-4-amine C21 H24 Cl N3 ZBFRXMWMJAMISF-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.276 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.631	α = 90
b = 61.631	β = 90
c = 342.247	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: 2020-08-26 
Deposition Author(s): Muenzker, L., Petrick, J.K., Schleberger, C., Jahnke, W.

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

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description