3W87

Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with SH-1-103


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with SH-1-103

Inaoka, D.K.Hashimoto, S.Rocha, J.R.Iida, M.Tabuchi, T.Lee, N.Matsuoka, S.Kuranaga, T.Shiba, T.Balogun, E.O.Sakamoto, K.Suzuki, S.Montanari, C.A.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
314Trypanosoma 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
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

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AB [auth B],
S [auth A]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
W87
Query on W87

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C [auth A],
LA [auth B]
5-{4-[5-(methoxycarbonyl)naphthalen-2-yl]butyl}-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
C21 H20 N2 O6
ILXUNLFRSXVJJZ-UHFFFAOYSA-N
NCO
Query on NCO

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JA [auth A],
KA [auth A]
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-UHFFFAOYSA-N
CAC
Query on CAC

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Q [auth A],
R [auth A],
YA [auth B],
ZA [auth B]
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
PEG
Query on PEG

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HA [auth A],
IA [auth A],
LB [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-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],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
MA [auth B],
N [auth A],
NA [auth B],
O [auth A],
OA [auth B],
P [auth A],
PA [auth B],
QA [auth B],
RA [auth B],
SA [auth B],
TA [auth B],
UA [auth B],
VA [auth B],
WA [auth B],
XA [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

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AA [auth A]
BA [auth A]
BB [auth B]
CA [auth A]
CB [auth B]
AA [auth A],
BA [auth A],
BB [auth B],
CA [auth A],
CB [auth B],
DA [auth A],
DB [auth B],
EA [auth A],
EB [auth B],
FA [auth A],
FB [auth B],
GA [auth A],
GB [auth B],
HB [auth B],
IB [auth B],
JB [auth B],
KB [auth B],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.934α = 90
b = 71.484β = 90
c = 129.646γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary