3W88

Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with SH-1-200

PDB DOI: https://doi.org/10.2210/pdb3W88/pdb

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

Deposited: 2013-03-12 Released: 2014-03-12
Deposition Author(s): 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.166
R-Value Work: 0.139
R-Value Observed: 0.140

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-1-200

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.

Macromolecule Content

Total Structure Weight: 75.96 kDa
Atom Count: 6,466
Modelled Residue Count: 628
Deposited Residue Count: 628
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 GB [auth B] SDF format, chain S [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain S [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain S [auth A]	GB [auth B], S [auth A]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain GB [auth B] Focus chain S [auth A] Interactions & Density Focus chain GB [auth B] Focus chain S [auth A]
W88 Query on W88 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain SA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain SA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain SA [auth B]	C [auth A], SA [auth B]	5-[4-(6-carboxynaphthalen-2-yl)butyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid C₂₀ H₁₈ N₂ O₆ DCZIJZIECAAXJK-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain SA [auth B] Interactions & Density Focus chain C [auth A] Focus chain SA [auth B]
NCO Query on NCO Download Ideal Coordinates CCD File SDF format, chain QA [auth A] SDF format, chain RA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain RA [auth A]	QA [auth A], RA [auth A]	COBALT HEXAMMINE(III) Co H₁₈ N₆ DYLMFCCYOUSRTK-UHFFFAOYSA-N		Interactions Focus chain QA [auth A] Focus chain RA [auth A] Interactions & Density Focus chain QA [auth A] Focus chain RA [auth A]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain EB [auth B] SDF format, chain FB [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain FB [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] mmCIF format, chain EB [auth B] mmCIF format, chain FB [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A]	EB [auth B], FB [auth B], Q [auth A], R [auth A]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain EB [auth B] Focus chain FB [auth B] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain EB [auth B] Focus chain FB [auth B] Focus chain Q [auth A] Focus chain R [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain WB [auth B] SDF format, chain XB [auth B] SDF format, chain YB [auth B] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain WB [auth B] MOL2 format, chain XB [auth B] MOL2 format, chain YB [auth B] mmCIF format, chain LA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain WB [auth B] mmCIF format, chain XB [auth B] mmCIF format, chain YB [auth B]	LA [auth A] MA [auth A] NA [auth A] OA [auth A] PA [auth A] LA [auth A], MA [auth A], NA [auth A], OA [auth A], PA [auth A], WB [auth B], XB [auth B], YB [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain WB [auth B] Focus chain XB [auth B] Focus chain YB [auth B] Interactions & Density Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain WB [auth B] Focus chain XB [auth B] Focus chain YB [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain BB [auth B] SDF format, chain CB [auth B] SDF format, chain D [auth A] SDF format, chain DB [auth B] SDF format, chain E [auth A] 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 J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain XA [auth B] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] MOL2 format, chain AB [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain D [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain E [auth A] 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 J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B] mmCIF format, chain AB [auth B] mmCIF format, chain BB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain D [auth A] mmCIF format, chain DB [auth B] mmCIF format, chain E [auth A] 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 J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain YA [auth B] mmCIF format, chain ZA [auth B]	AB [auth B] BB [auth B] CB [auth B] D [auth A] DB [auth B] AB [auth B], BB [auth B], CB [auth B], D [auth A], DB [auth B], 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], N [auth A], O [auth A], P [auth A], TA [auth B], UA [auth B], VA [auth B], WA [auth B], XA [auth B], YA [auth B], ZA [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain D [auth A] Focus chain DB [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain D [auth A] Focus chain DB [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain HB [auth B] SDF format, chain IA [auth A] SDF format, chain IB [auth B] SDF format, chain JA [auth A] SDF format, chain JB [auth B] SDF format, chain KA [auth A] SDF format, chain KB [auth B] SDF format, chain LB [auth B] SDF format, chain MB [auth B] SDF format, chain NB [auth B] SDF format, chain OB [auth B] SDF format, chain PB [auth B] SDF format, chain QB [auth B] SDF format, chain RB [auth B] SDF format, chain SB [auth B] SDF format, chain T [auth A] SDF format, chain TB [auth B] SDF format, chain U [auth A] SDF format, chain UB [auth B] SDF format, chain V [auth A] SDF format, chain VB [auth B] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain LB [auth B] MOL2 format, chain MB [auth B] MOL2 format, chain NB [auth B] MOL2 format, chain OB [auth B] MOL2 format, chain PB [auth B] MOL2 format, chain QB [auth B] MOL2 format, chain RB [auth B] MOL2 format, chain SB [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TB [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UB [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VB [auth B] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth B] mmCIF format, chain IA [auth A] mmCIF format, chain IB [auth B] mmCIF format, chain JA [auth A] mmCIF format, chain JB [auth B] mmCIF format, chain KA [auth A] mmCIF format, chain KB [auth B] mmCIF format, chain LB [auth B] mmCIF format, chain MB [auth B] mmCIF format, chain NB [auth B] mmCIF format, chain OB [auth B] mmCIF format, chain PB [auth B] mmCIF format, chain QB [auth B] mmCIF format, chain RB [auth B] mmCIF format, chain SB [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TB [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UB [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VB [auth B] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth A] AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], HB [auth B], IA [auth A], IB [auth B], JA [auth A], JB [auth B], KA [auth A], KB [auth B], LB [auth B], MB [auth B], NB [auth B], OB [auth B], PB [auth B], QB [auth B], RB [auth B], SB [auth B], T [auth A], TB [auth B], U [auth A], UB [auth B], V [auth A], VB [auth B], W [auth A], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain KA [auth A] Focus chain KB [auth B] Focus chain LB [auth B] Focus chain MB [auth B] Focus chain NB [auth B] Focus chain OB [auth B] Focus chain PB [auth B] Focus chain QB [auth B] Focus chain RB [auth B] Focus chain SB [auth B] Focus chain T [auth A] Focus chain TB [auth B] Focus chain U [auth A] Focus chain UB [auth B] Focus chain V [auth A] Focus chain VB [auth B] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain KA [auth A] Focus chain KB [auth B] Focus chain LB [auth B] Focus chain MB [auth B] Focus chain NB [auth B] Focus chain OB [auth B] Focus chain PB [auth B] Focus chain QB [auth B] Focus chain RB [auth B] Focus chain SB [auth B] Focus chain T [auth A] Focus chain TB [auth B] Focus chain U [auth A] Focus chain UB [auth B] Focus chain V [auth A] Focus chain VB [auth B] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.166
R-Value Work: 0.139
R-Value Observed: 0.140
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.974	α = 90
b = 71.518	β = 90
c = 129.537	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-03-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-03-12
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: 2024-10-09
Changes: Structure summary