3W1A

Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with 5-halogenated orotate derivatives


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with 5-halogenated orotate derivatives

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.Harada, S.Kita, K.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (fumarate)
A, B
313Trypanosoma cruzi strain CL BrenerMutation(s): 0 
Gene Names: DHOD
EC: 1.3.98.1
UniProt
Find proteins for Q4D3W2 (Trypanosoma cruzi (strain CL Brener))
Explore Q4D3W2 
Go to UniProtKB:  Q4D3W2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4D3W2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
FOT
Query on FOT

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
5-FLUORO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
C5 H3 F N2 O4
SEHFUALWMUWDKS-UHFFFAOYSA-N
NCO
Query on NCO

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D [auth A]COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
K [auth B]
L [auth B]
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: 1.42 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.24α = 90
b = 71.819β = 90
c = 123.775γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description