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- PDB-6aoh: Crystal structure of Toxoplasma gondii TS-DHFR complexed with NAD... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6aoh | ||||||
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Title | Crystal structure of Toxoplasma gondii TS-DHFR complexed with NADPH, dUMP, PDDF, and 5-(4-(3-(2-methoxypyrimidin-5-yl)phenyl)piperazin-1-yl)pyrimidine-2,4-diamine (TRC-2533) | ||||||
![]() | Bifunctional dihydrofolate reductase-thymidylate synthase | ||||||
![]() | OXIDOREDUCTASE / Toxoplasma gondii / Pyrimethamine / DHFR | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Thomas, S.B. / Li, Y. / Chen, Z. / Lu, H. | ||||||
![]() | ![]() Title: Identification of selective, brain penetrant Toxoplasma gondii dihydrofolate reductase inhibitors for the treatment of toxoplasmosis Authors: Thomas, S.B. / Hopper, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 223.8 KB | Display | ![]() |
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PDB format | ![]() | 176.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6aogC ![]() 6aoiC ![]() 4eilS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 64214.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q07422, dihydrofolate reductase, thymidylate synthase #2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.2 M ammonium citrate, pH 4.6, 15% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979282 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 11564 / % possible obs: 62.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 12 |
Reflection shell | Resolution: 3.5→3.63 Å / Rmerge(I) obs: 0.523 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4EIL Resolution: 3.5→50 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.858 / Cross valid method: THROUGHOUT / ESU R Free: 0.953
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.492 Å2
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Refinement step | Cycle: 1 / Resolution: 3.5→50 Å
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Refine LS restraints |
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