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Yorodumi- PDB-6kot: Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kot | |||||||||
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Title | Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with B12128 and NADPH | |||||||||
Components | Bifunctional dihydrofolate reductase-thymidylate synthase | |||||||||
Keywords | OXIDOREDUCTASE / TRANSFERASE / quadruple mutant dihydrofolate reductase / inhibitor / plasmodium falciparum | |||||||||
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 Similarity search - Function | |||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.149 Å | |||||||||
Authors | Vanichtanankul, J. / Vitsupakorn, D. | |||||||||
Funding support | Thailand, 2items
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Citation | Journal: Bioorg.Med.Chem. / Year: 2019 Title: 6-Hydrophobic aromatic substituent pyrimethamine analogues as potential antimalarials for pyrimethamine-resistant Plasmodium falciparum. Authors: Saepua, S. / Sadorn, K. / Vanichtanankul, J. / Anukunwithaya, T. / Rattanajak, R. / Vitsupakorn, D. / Kamchonwongpaisan, S. / Yuthavong, Y. / Thongpanchang, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kot.cif.gz | 249.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kot.ent.gz | 190.7 KB | Display | PDB format |
PDBx/mmJSON format | 6kot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kot_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 6kot_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 6kot_validation.xml.gz | 43.8 KB | Display | |
Data in CIF | 6kot_validation.cif.gz | 61.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/6kot ftp://data.pdbj.org/pub/pdb/validation_reports/ko/6kot | HTTPS FTP |
-Related structure data
Related structure data | 6kp2C 6kp7C 6kprC 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 BL21(DE3) (bacteria) / 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: 2.71 Å3/Da / Density % sol: 54.59 % |
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Crystal grow | Temperature: 297 K / Method: microbatch / pH: 4.5 / Details: NaOAc, NH2OAc, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.149→50 Å / Num. obs: 67136 / % possible obs: 85 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.033 / Rrim(I) all: 0.067 / Net I/σ(I): 19.75 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.403 / Num. unique obs: 70259 / CC1/2: 0.908 / % possible all: 86.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DP3 Resolution: 2.149→45.047 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.188 / SU B: 5.261 / SU ML: 0.135 / Average fsc free: 0.9104 / Average fsc work: 0.9281 / Cross valid method: NONE / ESU R: 0.266 / ESU R Free: 0.221 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 / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.803 Å2
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Refinement step | Cycle: LAST / Resolution: 2.149→45.047 Å
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Refine LS restraints |
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LS refinement shell |
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