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Yorodumi- PDB-8jfb: V1/S quadruple mutant Plasmodium falciparum dihydrofolate reducta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jfb | ||||||
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Title | V1/S quadruple mutant Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with compound 4 (B21588), NADPH and dUMP | ||||||
Components | Bifunctional dihydrofolate reductase-thymidylate synthase | ||||||
Keywords | OXIDOREDUCTASE / DHFR / dihydrofolate reductase / Plasmodium falciparum / malaria | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Vanichtanankul, J. / Saeyang, T. / Vitsupakorn, D. / Saepua, S. / Thongpanchang, C. / Yuthavong, Y. / Kamchonwongpaisan, S. / Hoarau, M. | ||||||
Funding support | Thailand, 1items
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Citation | Journal: Rsc Med Chem / Year: 2023 Title: Discovery of rigid biphenyl Plasmodium falciparum DHFR inhibitors using a fragment linking strategy. Authors: Hoarau, M. / Sermmai, P. / Varatthan, T. / Thiabma, R. / Jantra, T. / Rattanajak, R. / Vitsupakorn, D. / Vanichtanankul, J. / Saepua, S. / Yuthavong, Y. / Thongpanchang, C. / Kamchonwongpaisan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jfb.cif.gz | 295 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jfb.ent.gz | 189.8 KB | Display | PDB format |
PDBx/mmJSON format | 8jfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/8jfb ftp://data.pdbj.org/pub/pdb/validation_reports/jf/8jfb | HTTPS FTP |
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-Related structure data
Related structure data | 8jfcC 8jfdC 4dp3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 / Mutation: N51I, C59R, S108N, I164L 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: 3.03 Å3/Da / Density % sol: 59.37 % |
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Crystal grow | Temperature: 297 K / Method: microbatch / Details: PEG3350, Sodium malonate, pH5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å |
Detector | Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Mar 23, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→16.32 Å / Num. obs: 41800 / % possible obs: 93.15 % / Redundancy: 2.82 % / Biso Wilson estimate: 34.14 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 8.38 |
Reflection shell | Resolution: 2.65→2.75 Å / Rmerge(I) obs: 0.3949 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 2143 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DP3 Resolution: 2.65→16.32 Å / SU ML: 0.3782 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.5555 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: 37.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→16.32 Å
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Refine LS restraints |
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LS refinement shell |
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