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Yorodumi- PDB-7pnl: Complex between monomolecular human telomeric G-quadruplex and a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pnl | |||||||||
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Title | Complex between monomolecular human telomeric G-quadruplex and a sulfonamide derivative of the natural alkaloid Berberine | |||||||||
Components | G-guadruplex DNA (23-mer) | |||||||||
Keywords | DNA / DRUG-DNA COMPLEX / telomeric G-quadruplex | |||||||||
Function / homology | Chem-7VE / : / DNA / DNA (> 10) Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | |||||||||
Authors | Bazzicalupi, C. / Gratteri, P. / Petreni, A. / Nocentini, A. | |||||||||
Funding support | 2items
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Citation | Journal: J Enzyme Inhib Med Chem / Year: 2024 Title: Development of a multi-targeted chemotherapeutic approach based on G-quadruplex stabilisation and carbonic anhydrase inhibition. Authors: Nocentini, A. / Di Porzio, A. / Bonardi, A. / Bazzicalupi, C. / Petreni, A. / Biver, T. / Bua, S. / Marzano, S. / Amato, J. / Pagano, B. / Iaccarino, N. / De Tito, S. / Amente, S. / Supuran, ...Authors: Nocentini, A. / Di Porzio, A. / Bonardi, A. / Bazzicalupi, C. / Petreni, A. / Biver, T. / Bua, S. / Marzano, S. / Amato, J. / Pagano, B. / Iaccarino, N. / De Tito, S. / Amente, S. / Supuran, C.T. / Randazzo, A. / Gratteri, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pnl.cif.gz | 28.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pnl.ent.gz | 18.4 KB | Display | PDB format |
PDBx/mmJSON format | 7pnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pnl_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7pnl_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7pnl_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 7pnl_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/7pnl ftp://data.pdbj.org/pub/pdb/validation_reports/pn/7pnl | HTTPS FTP |
-Related structure data
Related structure data | 6h5rS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: DNA chain | Mass: 7287.690 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 65.24 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: KCl, potassium Cacodylate, MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→36.36 Å / Num. obs: 6268 / % possible obs: 98.8 % / Redundancy: 3.27 % / CC1/2: 0.998 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.046 / Net I/σ(I): 13.73 |
Reflection shell | Resolution: 1.83→1.94 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1996 / CC1/2: 0.891 / Rrim(I) all: 0.779 / Χ2: 0.57 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6H5R Resolution: 1.83→36.36 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.784 / SU ML: 0.13 / SU R Cruickshank DPI: 0.1535 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 163.54 Å2 / Biso mean: 56.126 Å2 / Biso min: 28.76 Å2
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Refinement step | Cycle: final / Resolution: 1.83→36.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.877 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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