3W1M

Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with 5-bromoorotate

• PDB DOI: https://doi.org/10.2210/pdb3W1M/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Trypanosoma cruzi strain CL Brener
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-11-16 Released: 2013-11-20 
• Deposition Author(s): Inaoka, D.K., Iida, M., Tabuchi, T., Lee, N., Matsuoka, S., Shiba, T., Sakamoto, K., Suzuki, S., Balogun, E.O., Nara, T., Aoki, T., Inoue, M., Honma, T., Tanaka, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.183 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 

Literature

Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with 5-bromoorotate

Inaoka, D.K., Iida, M., Tabuchi, T., Lee, N., Matsuoka, S., Shiba, T., Sakamoto, K., Suzuki, S., Balogun, E.O., Nara, T., Aoki, T., Inoue, M., Honma, T., Tanaka, A.

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: 70.23 kDa 
• Atom Count: 5,544 
• Modelled Residue Count: 626 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase (fumarate)	A, B	313	Trypanosoma cruzi strain CL Brener	Mutation(s): 0  Gene Names: PyrD EC: 1.3.98.1
UniProt
Find proteins for Q4D3W2 (Trypanosoma cruzi (strain CL Brener)) Explore Q4D3W2  Go to UniProtKB:  Q4D3W2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], I [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
RRO	E [auth A], J [auth B]	5-bromo-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid C5 H3 Br N2 O4 YQYHIPBLZSIHDI-UHFFFAOYSA-N
NCO	D [auth A]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N
GOL	F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.183 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.341	α = 90
b = 71.912	β = 90
c = 123.849	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-20 
Deposition Author(s): Inaoka, D.K., Iida, M., Tabuchi, T., Lee, N., Matsuoka, S., Shiba, T., Sakamoto, K., Suzuki, S., Balogun, E.O., Nara, T., Aoki, T., Inoue, M., Honma, T., Tanaka, A.

Revision History  

• Version 1.0: 2013-11-20
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description