2DJL | pdb_00002djl

Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with succinate

• PDB DOI: https://doi.org/10.2210/pdb2DJL/pdb

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


• Deposited: 2006-04-04 Released: 2007-06-26 
• Deposition Author(s): Inaoka, D.K., Shimizu, H., Sakamoto, K., Shiba, T., Kurisu, G., Nara, T., Aoki, T., Harada, S., Kita, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 
  0.183 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with succinate

Inaoka, D.K., Shimizu, H., Sakamoto, K., Shiba, T., Kurisu, G., Nara, T., Aoki, T., Harada, S., Kita, K.

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: 70.2 kDa 
• Atom Count: 5,568 
• Modeled Residue Count: 624 
• Deposited Residue Count: 628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dihydroorotate dehydrogenase	A, B	314	Trypanosoma cruzi	Mutation(s): 0  Gene Names: TCDHOD2 EC: 1.3.3.1 (PDB Primary Data), 1.3.98.1 (UniProt)
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	D [auth A], J [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
NCO	C [auth A]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N
SIN	E [auth A], K [auth B]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
GOL	F [auth A], G [auth A], H [auth A], I [auth A], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free:  0.183 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.154	α = 90
b = 71.766	β = 90
c = 123.4	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-26 
Deposition Author(s): Inaoka, D.K., Shimizu, H., Sakamoto, K., Shiba, T., Kurisu, G., Nara, T., Aoki, T., Harada, S., Kita, K.

Revision History  

• Version 1.0: 2007-06-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary