3IRO | pdb_00003iro

Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase complexed with NADPH and Q-8 antifolate

PDB DOI: https://doi.org/10.2210/pdb3IRO/pdb

Classification: OXIDOREDUCTASE, TRANSFERASE
Organism(s): Trypanosoma cruzi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-08-24 Released: 2010-07-28
Deposition Author(s): Chitnumsub, P., Yuvaniyama, J., Yuthavong, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.277 (Depositor), 0.266 (DCC)
R-Value Work:
0.206 (Depositor), 0.198 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural basis of antifolate inhibition of Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase

Chitnumsub, P., Yuvaniyama, J., Vilaivan, T., Vanichtanankul, J., Kamchonwongpaisan, S., Yuthavong, Y.

To be published.

Macromolecule Content

Total Structure Weight: 241.16 kDa
Atom Count: 16,862
Modeled Residue Count: 2,062
Deposited Residue Count: 2,084
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional dihydrofolate reductase-thymidylate synthase	A, B, C, D	521	Trypanosoma cruzi	Mutation(s): 0 EC: 1.5.1.3 (PDB Primary Data), 2.1.1.45 (PDB Primary Data)
UniProt
Find proteins for Q27793 (Trypanosoma cruzi) Explore Q27793 Go to UniProtKB: Q27793
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q27793
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain X [auth D] SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain X [auth D] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain X [auth D] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	F [auth A], L [auth B], Q [auth C], X [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain X [auth D]
2CY Query on 2CY Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain P [auth C] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain W [auth D] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain W [auth D] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B], P [auth C], W [auth D]	5-[3-(3-fluorophenoxy)propoxy]quinazoline-2,4-diamine C₁₇ H₁₇ F N₄ O₂ WYNJMQXBACXTGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain W [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain M [auth B] SDF format, chain G [auth A] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A]	G [auth A], M [auth B], R [auth C], S [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain N [auth B]	N [auth B], T [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain T [auth C] Interactions & Density Focus chain N [auth B] Focus chain T [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain O [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] H [auth A] I [auth A] J [auth A] AA [auth D], BA [auth D], H [auth A], I [auth A], J [auth A], O [auth B], U [auth C], V [auth C], Y [auth D], Z [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.277 (Depositor), 0.266 (DCC)
R-Value Work: 0.206 (Depositor), 0.198 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.544	α = 90
b = 165.936	β = 113.41
c = 84.718	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-07-28

Deposition Author(s):

Chitnumsub, P.

Yuvaniyama, J.

Yuthavong, Y.

Revision History (Full details and data files)

Version 1.0: 2010-07-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2018-04-04
Changes: Data collection
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description