3W22

Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-3-125


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

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 MII-3-125

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: PyrD
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
2RO
Query on 2RO

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
5-[2-(4-tert-butylphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
C17 H20 N2 O4
SSILBIHZUGTHHN-UHFFFAOYSA-N
NCO
Query on NCO

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

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D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.058α = 90
b = 71.637β = 90
c = 129.293γ = 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: 2013-11-27
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description