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- PDB-6lhi: Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum di... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6lhi | ||||||
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Title | Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with C466 (compound 42) and NADPH | ||||||
![]() | Bifunctional dihydrofolate reductase-thymidylate synthase | ||||||
![]() | OXIDOREDUCTASE / Inhinitor / antifolate / dyhydrofolate reductase / plasmodium falciparum / ANTIBIOTIC | ||||||
Function / homology | ![]() thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / methylation / nucleotide binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Vanichtanankul, J. / Vitsupakorn, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Flexible diaminodihydrotriazine inhibitors of Plasmodium falciparum dihydrofolate reductase: Binding strengths, modes of binding and their antimalarial activities. Authors: Kamchonwongpaisan, S. / Charoensetakul, N. / Srisuwannaket, C. / Taweechai, S. / Rattanajak, R. / Vanichtanankul, J. / Vitsupakorn, D. / Arwon, U. / Thongpanchang, C. / Tarnchompoo, B. / ...Authors: Kamchonwongpaisan, S. / Charoensetakul, N. / Srisuwannaket, C. / Taweechai, S. / Rattanajak, R. / Vanichtanankul, J. / Vitsupakorn, D. / Arwon, U. / Thongpanchang, C. / Tarnchompoo, B. / Vilaivan, T. / Yuthavong, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 421.4 KB | Display | ![]() |
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PDB format | ![]() | 349.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 24.4 KB | Display | |
Data in CIF | ![]() | 36.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6leuC ![]() 6levC ![]() 6lezC ![]() 6lh9C ![]() 6lhjC ![]() 4dp3S S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 71908.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: DHFR-TS, V1/S / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 103 molecules ![](data/chem/img/MET.gif)
![](data/chem/img/UMP.gif)
![](data/chem/img/E9X.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UMP.gif)
![](data/chem/img/E9X.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MET / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.606 Å3/Da / Density % sol: 52.8 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 4.6 Details: 0.1M sodium acetate, pH 4.6, 0.2M ammonium acetate, 25% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Oct 9, 2003 |
Radiation | Monochromator: 1.5418 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→46.41 Å / Num. obs: 40994 / % possible obs: 90.8 % / Redundancy: 7.874 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.59→2.7 Å / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4171 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DP3 Resolution: 2.59→46.41 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.871 / Cross valid method: NONE / ESU R: 0.281 / ESU R Free: 0.087 Details: Hydrogens have been added in their riding positions
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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: 39.668 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→46.41 Å
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Refine LS restraints |
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LS refinement shell |
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