3IRN

Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase COMPLEXED WITH NADPH AND Cycloguanil

• PDB DOI: https://doi.org/10.2210/pdb3IRN/pdb

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


• Deposited: 2009-08-24 Released: 2010-07-28 
• Deposition Author(s): Chitnumsub, P., Yuvaniyama, J., Yuthavong, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.299 
• R-Value Work: 0.230 

Starting Model: experimental

Literature

Structural basis of antifolate inhibition of Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase

Chitnumsub, P., Yuvaniyama, J., Vilaivan, T., Vanichtanankul, J., Kamchonwongpaisan, S., Yuthavong, Y.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 240.08 kDa 
• Atom Count: 16,901 
• Modelled Residue Count: 2,061 
• Deposited Residue Count: 2,084 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional dihydrofolate reductase-thymidylate synthase	A, B, C, D	521	Trypanosoma cruzi	Mutation(s): 0  EC: 1.5.1.3 (PDB Primary Data), 2.1.1.45 (PDB Primary Data)
UniProt
Find proteins for Q27793 (Trypanosoma cruzi) Explore Q27793  Go to UniProtKB:  Q27793

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	F [auth A], J [auth B], L [auth C], O [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
1CY	E [auth A], I [auth B], K [auth C], N [auth D]	1-(4-chlorophenyl)-6,6-dimethyl-1,6-dihydro-1,3,5-triazine-2,4-diamine C11 H14 Cl N5 QMNFFXRFOJIOKZ-UHFFFAOYSA-N
PO4	G [auth A], H [auth A], M [auth C], P [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.299 
• R-Value Work: 0.230 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.345	α = 90
b = 165.593	β = 113.361
c = 84.848	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-28 
Deposition Author(s): Chitnumsub, P., Yuvaniyama, J., Yuthavong, Y.

Revision History  

• Version 1.0: 2010-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description