2E68

Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with dihydroorotate

PDB DOI: https://doi.org/10.2210/pdb2E68/pdb

Classification: OXIDOREDUCTASE
Organism(s): Trypanosoma cruzi
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2006-12-26 Released: 2008-01-15
Deposition Author(s): Inaoka, D.K., Shimizu, H., Sakamoto, K., Shiba, T., Kurisu, G., Nara, T., Aoki, T., Harada, S., Kita, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free:
0.183 (Depositor), 0.180 (DCC)
R-Value Work:
0.168 (Depositor), 0.170 (DCC)
R-Value Observed:
0.169 (Depositor)

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

Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with dihydroorotate

Inaoka, D.K., Shimizu, H., Sakamoto, K., Shiba, T., Kurisu, G., Nara, T., Aoki, T., Harada, S., Kita, K.

To be published.

Macromolecule Content

Total Structure Weight: 70.16 kDa
Atom Count: 5,603
Modelled Residue Count: 625
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	A, B	314	Trypanosoma cruzi	Mutation(s): 0 Gene Names: tcdhod2 EC: 1.3.3.1 (PDB Primary Data), 1.3.98.1 (UniProt)
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 LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	D [auth A], J [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
NCO Query on NCO Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	COBALT HEXAMMINE(III) Co H₁₈ N₆ DYLMFCCYOUSRTK-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
DOR Query on DOR Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B]	E [auth A], K [auth B]	(4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID C₅ H₆ N₂ O₄ UFIVEPVSAGBUSI-REOHCLBHSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [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] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free: 0.183 (Depositor), 0.180 (DCC)
R-Value Work: 0.168 (Depositor), 0.170 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.443	α = 90
b = 71.944	β = 90
c = 123.852	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-01-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-01-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary