6SDQ | pdb_00006sdq

Trypanosoma cruzi farnesyl diphosphate synthase in complex with fragment 2m5n

• PDB DOI: https://doi.org/10.2210/pdb6SDQ/pdb

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


• Deposited: 2019-07-29 Released: 2020-08-26 
• Deposition Author(s): Magari, F., Heine, A., Klebe, G.
• Funding Organization(s): European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Trypanosoma cruzi farnesyl diphosphate synthase in complex with fragment 2m5n

Magari, F., Heine, A., Klebe, G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering, mass spectrometry

Macromolecule Content 

• Total Structure Weight: 41.6 kDa 
• Atom Count: 3,139 
• Modeled Residue Count: 361 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl diphosphate synthase	A	362	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
L8Q (Subject of Investigation/LOI)	E [auth A]	2-methoxy-5-nitro-phenol C7 H7 N O4 KXKCTSZYNCDFFG-UHFFFAOYSA-N
SO4	B [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: 1.68 Å
• R-Value Free:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.919	α = 90
b = 57.919	β = 90
c = 398.079	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Magari, F., Heine, A., Klebe, G.

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Funding Organization	Location	Grant Number
European Union		--

Revision History  

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