3W7K

Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-6-066


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-6-066

Inaoka, D.K.Iida, M.Tabuchi, T.Lee, N.Hashimoto, S.Matsuoka, S.Kuranaga, T.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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroorotate dehydrogenase (fumarate)
A, B
313Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Gene Names: pyr4 (tcdhod2)
EC: 1.3.98.1
Find proteins for Q4D3W2 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4D3W2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

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Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
NCO
Query on NCO

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Download CCD File 
A
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
W7K
Query on W7K

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Download CCD File 
A, B
5-[2-(3,6-dimethoxynaphthalen-2-yl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
C19 H18 N2 O6
ZWWHFNCLURKBGD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.964α = 90.00
b = 71.627β = 90.00
c = 129.710γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description