5E93 | pdb_00005e93

Crystal Structure of Trypanosoma cruzi Dihydroorotate Dehydrogenase in Complex with Neq0071

PDB DOI: https://doi.org/10.2210/pdb5E93/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Trypanosoma cruzi strain CL Brener
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-10-14 Released: 2016-10-19
Deposition Author(s): Rocha, J.R., Inaoka, D.K., Cheleski, J., Shiba, T., Harada, S., Montanari, C.A., Kita, K.
Funding Organization(s): Creative Scientific Research, Japanese Society for the Promotion of Science, Science and Technology Research Partnership for Sustainable Development, Fundacao de Amparo a Pesquisa do Estado de Sao Paulo

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free:
0.168 (Depositor), 0.169 (DCC)
R-Value Work:
0.145 (Depositor), 0.145 (DCC)
R-Value Observed:
0.146 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Exploring Trypanosoma cruzi Dihydroorotate Dehydrogenase Active Site Plasticity for the Discovery of Potent and Selective Inhibitors with Trypanocidal Activity

Rocha, J.R., Cheleski, J., Inaoka, D.K., Avelar, L.A., Ribeiro, J.F.R., Wiggers, H.J., Albuquerque, S., Shiba, T., Harada, S., Kita, K., Silva, A.B.F., Montanari, C.A.

To be published.

Macromolecule Content

Total Structure Weight: 73.08 kDa
Atom Count: 5,936
Modeled Residue Count: 626
Deposited Residue Count: 628
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase (fumarate)	A, B	314	Trypanosoma cruzi strain CL Brener	Mutation(s): 0 Gene Names: PyrD, pyr4 EC: 1.3.98.1
UniProt
Find proteins for Q4D3W2 (Trypanosoma cruzi (strain CL Brener)) Explore Q4D3W2 Go to UniProtKB: Q4D3W2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4D3W2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain J [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain J [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain J [auth A]	FA [auth B], J [auth A]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain FA [auth B] Focus chain J [auth A] Interactions & Density Focus chain FA [auth B] Focus chain J [auth A]
5LL Query on 5LL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain Y [auth B] MOL2 format, chain C [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain C [auth A] mmCIF format, chain Y [auth B]	C [auth A], Y [auth B]	5-[(E)-3-(furan-2-yl)prop-2-enylidene]-1,3-diazinane-2,4,6-trione C₁₁ H₈ N₂ O₄ PRGJOMANJQAXIH-HNQUOIGGSA-N		Interactions Focus chain C [auth A] Focus chain Y [auth B] Interactions & Density Focus chain C [auth A] Focus chain Y [auth B]
NCO Query on NCO Download:Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain K [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain K [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain K [auth A]	GA [auth B], HA [auth B], K [auth A]	COBALT HEXAMMINE(III) Co H₁₈ N₆ DYLMFCCYOUSRTK-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain K [auth A] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain K [auth A]
CAC Query on CAC Download:Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A]	W [auth A], X [auth A]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain W [auth A] Focus chain X [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain UA [auth B] MOL2 format, chain UA [auth B] mmCIF format, chain UA [auth B]	UA [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain UA [auth B] Interactions & Density Focus chain UA [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain D [auth A] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] D [auth A] DA [auth B] AA [auth B], BA [auth B], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], G [auth A], H [auth A], I [auth A], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain Z [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain V [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A]	IA [auth B] JA [auth B] KA [auth B] L [auth A] LA [auth B] IA [auth B], JA [auth B], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], V [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain V [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free: 0.168 (Depositor), 0.169 (DCC)
R-Value Work: 0.145 (Depositor), 0.145 (DCC)
R-Value Observed: 0.146 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.325	α = 90
b = 71.789	β = 90
c = 124.343	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
MOLREP	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-10-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Creative Scientific Research	Japan	18GS0314
Japanese Society for the Promotion of Science	Japan	18073004, 26253025, 26870119
Science and Technology Research Partnership for Sustainable Development	Japan	10000284
Fundacao de Amparo a Pesquisa do Estado de Sao Paulo	Brazil	2010/20021-4, 2012/01777-6

Revision History (Full details and data files)

Version 1.0: 2016-10-19
Type: Initial release
Version 1.1: 2020-02-19
Changes: Data collection, Derived calculations
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Structure summary