5QTH | pdb_00005qth

T. brucei FPPS in complex with CID 2799882

• PDB DOI: https://doi.org/10.2210/pdb5QTH/pdb
• Deposition Group: G_1002102 (changed state) ExploreG_1002102

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


• Deposited: 2019-08-09 Released: 2020-10-07 
• Deposition Author(s): Muenzker, L., Petrick, J.K., Schleberger, C., Cornaciu, I., Marquez, J.A., Jahnke, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.283 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Literature

T. brucei FPPS in complex with CID 2799882

Muenzker, L.

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: 42.65 kDa 
• Atom Count: 2,769 
• Modeled Residue Count: 329 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PJY	E [auth A]	N,N-dimethyl-2-(methylsulfanyl)pyridine-3-carboxamide C9 H12 N2 O S KORZBTDVYBSAMM-UHFFFAOYSA-N
PO4	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.283 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.556	α = 90
b = 60.556	β = 90
c = 339.825	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-07 
Deposition Author(s): Muenzker, L., Petrick, J.K., Schleberger, C., Cornaciu, I., Marquez, J.A., Jahnke, W.

Revision History  

• Version 1.0: 2020-10-07
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references