+Open data
-Basic information
Entry | Database: PDB / ID: 6a7c | ||||||
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Title | Human dihydrofolate reductase complexed with NADPH and BT1 | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / DHFR / antifolate / inhibitor | ||||||
Function / homology | Function and homology information regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / tetrahydrofolate biosynthetic process / mRNA regulatory element binding translation repressor activity / positive regulation of nitric-oxide synthase activity / one-carbon metabolic process / NADP binding / negative regulation of translation / mRNA binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Vanichtanankul, J. / Tarnchompoo, B. / Chitnumsub, P. / Kamchonwongpaisan, S. / Yuthavong, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: ACS Med Chem Lett / Year: 2018 Title: Hybrid Inhibitors of Malarial Dihydrofolate Reductase with Dual Binding Modes That Can Forestall Resistance. Authors: Tarnchompoo, B. / Chitnumsub, P. / Jaruwat, A. / Shaw, P.J. / Vanichtanankul, J. / Poen, S. / Rattanajak, R. / Wongsombat, C. / Tonsomboon, A. / Decharuangsilp, S. / Anukunwithaya, T. / ...Authors: Tarnchompoo, B. / Chitnumsub, P. / Jaruwat, A. / Shaw, P.J. / Vanichtanankul, J. / Poen, S. / Rattanajak, R. / Wongsombat, C. / Tonsomboon, A. / Decharuangsilp, S. / Anukunwithaya, T. / Arwon, U. / Kamchonwongpaisan, S. / Yuthavong, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a7c.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a7c.ent.gz | 41.3 KB | Display | PDB format |
PDBx/mmJSON format | 6a7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a7c_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6a7c_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6a7c_validation.xml.gz | 12 KB | Display | |
Data in CIF | 6a7c_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/6a7c ftp://data.pdbj.org/pub/pdb/validation_reports/a7/6a7c | HTTPS FTP |
-Related structure data
Related structure data | 6a2kC 6a2lC 6a2mC 6a2nC 6a2oC 6a2pC 6a7eC 4ddrS 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: 21349.525 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHFR / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00374, dihydrofolate reductase | ||
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#2: Chemical | ChemComp-NDP / | ||
#3: Chemical | ChemComp-9QO / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.81 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: 2.7 M Ammonium sulphate, 100 mM K2HPO4, 3%(v/v) Ethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→30 Å / Num. obs: 12165 / % possible obs: 99.6 % / Redundancy: 3.62 % / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.06→2.13 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DDR Resolution: 2.06→26.35 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.564 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.198
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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 max: 80.78 Å2 / Biso mean: 28.022 Å2 / Biso min: 10.73 Å2
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Refinement step | Cycle: final / Resolution: 2.06→26.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.061→2.115 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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