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- PDB-9xio: Toxoplasma gondii dihydrofolate reductase thymidylate synthase (T... -

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Basic information

Entry
Database: PDB / ID: 9xio
TitleToxoplasma gondii dihydrofolate reductase thymidylate synthase (TgDHFR-TS) complexed with P218, NADPH and dUMP
ComponentsBifunctional dihydrofolate reductase-thymidylate synthase
KeywordsOXIDOREDUCTASE / dihydrofolate reductase / Toxoplasma gondii / P218
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase / one-carbon metabolic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / mitochondrion / cytosol
Similarity search - Function
Bifunctional dihydrofolate reductase/thymidylate synthase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. ...Bifunctional dihydrofolate reductase/thymidylate synthase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
Chem-MMV / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Bifunctional dihydrofolate reductase-thymidylate synthase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVanichtanankul, J. / Saeyang, T. / Yuthavong, Y. / Kamchonwongpaisan, S.
Funding support Thailand, 1items
OrganizationGrant numberCountry
The Thailand Research Fund (TRF)TRG5780138 Thailand
CitationJournal: Eur.J.Med.Chem. / Year: 2026
Title: Repurpose antimalarials to target Toxoplasma gondii dihydrofolate reductase thymidylate synthase.
Authors: Decharuangsilp, S. / Koompapong, K. / Arwon, U. / Tuyapala, N. / Hoarau, M. / Tanasugarn, L. / Pengon, J. / Talawanich, Y. / Saeyang, T. / Vanichtanankul, J. / Yuthavong, Y. / ...Authors: Decharuangsilp, S. / Koompapong, K. / Arwon, U. / Tuyapala, N. / Hoarau, M. / Tanasugarn, L. / Pengon, J. / Talawanich, Y. / Saeyang, T. / Vanichtanankul, J. / Yuthavong, Y. / Kamchonwongpaisan, S. / Mahittikorn, A. / Kongkasuriyachai, D.
History
DepositionNov 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional dihydrofolate reductase-thymidylate synthase
B: Bifunctional dihydrofolate reductase-thymidylate synthase
C: Bifunctional dihydrofolate reductase-thymidylate synthase
D: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,01916
Polymers275,3714
Non-polymers5,64812
Water8,323462
1
A: Bifunctional dihydrofolate reductase-thymidylate synthase
B: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,5098
Polymers137,6852
Non-polymers2,8246
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11030 Å2
ΔGint-68 kcal/mol
Surface area44280 Å2
MethodPISA
2
C: Bifunctional dihydrofolate reductase-thymidylate synthase
D: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,5098
Polymers137,6852
Non-polymers2,8246
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10810 Å2
ΔGint-62 kcal/mol
Surface area44130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.168, 93.339, 116.989
Angle α, β, γ (deg.)83.70, 80.67, 80.25
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Bifunctional dihydrofolate reductase-thymidylate synthase / DHFR-TS


Mass: 68842.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q07422, dihydrofolate reductase, thymidylate synthase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-MMV / 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid


Mass: 360.408 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H24N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 0.2 M lithium nitrate, 14% (w/v) PEG4000 and 0.1 M bis-Tris propane pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→35.65 Å / Num. obs: 83670 / % possible obs: 85.46 % / Redundancy: 2.1 % / Biso Wilson estimate: 37.08 Å2 / CC1/2: 0.868 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.051 / Rrim(I) all: 0.075 / Net I/σ(I): 10.9
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 5561 / CC1/2: 0.868 / CC star: 0.964

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→35.65 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 4215 5.04 %
Rwork0.1719 --
obs0.1752 83654 85.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→35.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17431 0 376 462 18269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918248
X-RAY DIFFRACTIONf_angle_d1.02624736
X-RAY DIFFRACTIONf_dihedral_angle_d15.9986796
X-RAY DIFFRACTIONf_chiral_restr0.0542662
X-RAY DIFFRACTIONf_plane_restr0.013181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.3416700.22921494X-RAY DIFFRACTION48
2.53-2.560.32971080.22931795X-RAY DIFFRACTION58
2.56-2.590.3353800.22182014X-RAY DIFFRACTION64
2.59-2.620.32871000.21941985X-RAY DIFFRACTION65
2.62-2.660.30291270.22182144X-RAY DIFFRACTION68
2.66-2.690.27651230.22222175X-RAY DIFFRACTION73
2.69-2.730.34671240.21362382X-RAY DIFFRACTION76
2.73-2.770.30881180.20742431X-RAY DIFFRACTION78
2.77-2.820.31491410.2192593X-RAY DIFFRACTION85
2.82-2.860.30311330.21272784X-RAY DIFFRACTION88
2.86-2.910.2851420.21112868X-RAY DIFFRACTION92
2.91-2.970.24821510.21482924X-RAY DIFFRACTION96
2.97-3.020.29391740.21183004X-RAY DIFFRACTION97
3.02-3.080.25611710.21472965X-RAY DIFFRACTION96
3.08-3.150.28051530.21213011X-RAY DIFFRACTION96
3.15-3.220.29681640.19742966X-RAY DIFFRACTION96
3.22-3.310.25761740.18962960X-RAY DIFFRACTION96
3.31-3.390.2541600.17992930X-RAY DIFFRACTION96
3.39-3.490.26531480.18062967X-RAY DIFFRACTION95
3.49-3.610.24651500.17892938X-RAY DIFFRACTION95
3.61-3.740.24421700.18692907X-RAY DIFFRACTION94
3.74-3.890.21581450.16362909X-RAY DIFFRACTION94
3.89-4.060.22691610.15582911X-RAY DIFFRACTION93
4.06-4.280.18281520.13962816X-RAY DIFFRACTION91
4.28-4.540.17071440.12322776X-RAY DIFFRACTION90
4.54-4.890.16721470.11942809X-RAY DIFFRACTION90
4.89-5.380.19131510.13752699X-RAY DIFFRACTION88
5.38-6.160.22771750.15512884X-RAY DIFFRACTION94
6.16-7.750.19511350.15632866X-RAY DIFFRACTION92
7.75-35.650.18381240.14122532X-RAY DIFFRACTION82

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