9OBB | pdb_00009obb

Crystal structure of dihydroorotate dehydrogenase from Leishmania brasiliensis in complex with 5-[(E)-3-(p-methoxyphenyl)-2-propenylidene]-2,4,6(1H,3H,5H)-pyrimidinetrione

• PDB DOI: https://doi.org/10.2210/pdb9OBB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Leishmania braziliensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-04-22 Released: 2026-05-06 
• Deposition Author(s): Vaidergorn, M.M., Nonato, M.C., Froes, T.Q., Augusto, B.S.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.245 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of dihydroorotate dehydrogenase from Leishmania brasiliensis in complex with 5-[(E)-3-(p-methoxyphenyl)-2-propenylidene]-2,4,6(1H,3H,5H)-pyrimidinetrione

Vaidergorn, M.M., Nonato, M.C., Froes, T.Q., Augusto, B.S.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 76.26 kDa 
• Atom Count: 4,758 
• Modeled Residue Count: 624 
• Deposited Residue Count: 694 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase	A, B	347	Leishmania braziliensis	Mutation(s): 0  Gene Names: DHODH, LBRM_16_0550 EC: 1.3.3.1 (PDB Primary Data), 1.3.98.1 (UniProt)
UniProt
Find proteins for E9AI53 (Leishmania braziliensis) Explore E9AI53  Go to UniProtKB:  E9AI53

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], E [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
5TI (Subject of Investigation/LOI)	D [auth A], F [auth B]	5-[3-(4-methoxyphenyl)prop-2-enylidene]-1,3-diazinane-2,4,6-trione C14 H12 N2 O4 IXYLVJHFJKDHRM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.245 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.644	α = 90
b = 104.595	β = 90
c = 106.609	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
pointless	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-06 
Deposition Author(s): Vaidergorn, M.M., Nonato, M.C., Froes, T.Q., Augusto, B.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5R01AI160379

Revision History  

• Version 1.0: 2026-05-06
  Type: Initial release