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Yorodumi- PDB-6lev: Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lev | ||||||
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Title | Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with compound 46 and NADPH | ||||||
Components | Bifunctional dihydrofolate reductase-thymidylate synthase | ||||||
Keywords | OXIDOREDUCTASE / Inhinitor / antifolate / dyhydrofolate reductase / plasmodium falciparum / ANTIBIOTIC | ||||||
Function / homology | Function and homology information 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 | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.644 Å | ||||||
Authors | Vanichtanankul, J. / Vitsupakorn, D. | ||||||
Funding support | Thailand, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lev.cif.gz | 240.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lev.ent.gz | 185.3 KB | Display | PDB format |
PDBx/mmJSON format | 6lev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lev_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6lev_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6lev_validation.xml.gz | 40.9 KB | Display | |
Data in CIF | 6lev_validation.cif.gz | 55.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/6lev ftp://data.pdbj.org/pub/pdb/validation_reports/le/6lev | HTTPS FTP |
-Related structure data
Related structure data | 6leuC 6lezC 6lh9C 6lhiC 6lhjC 4dp3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 71908.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: DHFR-TS, V1/S / Production host: Escherichia coli (E. coli) / References: UniProt: D9N170 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.64 % |
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Crystal grow | Temperature: 297 K / Method: microbatch / pH: 4.6 Details: 0.1 mM sodium acetate pH 4.6, 25% (w/v) PEG 4000, 0.2 M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Oct 9, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→10 Å / Num. obs: 45357 / % possible obs: 90.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.64→2.69 Å / Rmerge(I) obs: 0.445 / Num. unique obs: 6232 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DP3 Resolution: 2.644→10 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.897 / SU B: 13.149 / SU ML: 0.27 / Cross valid method: NONE / ESU R: 1.391 / ESU R Free: 0.375 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: 50.814 Å2
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Refinement step | Cycle: LAST / Resolution: 2.644→10 Å
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Refine LS restraints |
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LS refinement shell |
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