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- PDB-7fgw: Toxoplasma gondii dihydrofolate reductase thymidylate synthase (T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7fgw | ||||||
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Title | Toxoplasma gondii dihydrofolate reductase thymidylate synthase (TgDHFR-TS) complexed with pyrimethamine, NADPH and dUMP | ||||||
![]() | Bifunctional dihydrofolate reductase-thymidylate synthase | ||||||
![]() | OXIDOREDUCTASE / Pyrimethamine / Toxoplasma gondii / dihydrofolate reductase / thymidylate synthase | ||||||
Function / homology | ![]() thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / methylation / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vanichtanankul, J. / Yoomuang, A. / Taweechai, S. / Saeyang, T. / Yuvaniyama, Y. / Tarnchompoo, B. / Yuthavong, Y. / Kamchonwongpaisan, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Insight into Effective Inhibitors' Binding to Toxoplasma gondii Dihydrofolate Reductase Thymidylate Synthase. Authors: Vanichtanankul, J. / Yoomuang, A. / Taweechai, S. / Saeyang, T. / Pengon, J. / Yuvaniyama, J. / Tarnchompoo, B. / Yuthavong, Y. / Kamchonwongpaisan, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 609.9 KB | Display | ![]() |
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PDB format | ![]() | 398.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7fgxC ![]() 7fgyC ![]() 7xi7C ![]() 4eilS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 68842.656 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q07422, dihydrofolate reductase, thymidylate synthase |
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-Non-polymers , 5 types, 1545 molecules ![](data/chem/img/NDP.gif)
![](data/chem/img/CP6.gif)
![](data/chem/img/BEN.gif)
![](data/chem/img/UMP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CP6.gif)
![](data/chem/img/BEN.gif)
![](data/chem/img/UMP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-CP6 / #4: Chemical | #5: Chemical | ChemComp-UMP / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.57 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M Lithium nitrate, 14% (w/v) PEG4000, 0.1 M Bis-Tris propane pH 7.5 and 1% (w/v) benzamidine hydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. obs: 152902 / % possible obs: 96.3 % / Redundancy: 2.2 % / Biso Wilson estimate: 25.68 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 2 % / Rmerge(I) obs: 0.243 / Num. unique obs: 14023 / % possible all: 88.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4EIL Resolution: 2.15→29.29 Å / SU ML: 0.2316 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.0867 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→29.29 Å
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Refine LS restraints |
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LS refinement shell |
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