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Yorodumi- PDB-8aad: Two carbons pendant pyridine derivative of the natural alkaloid B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aad | |||||||||
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Title | Two carbons pendant pyridine derivative of the natural alkaloid Berberine as Human Telomeric G-quadruplex Binder | |||||||||
Components | DNA TAGGGTTAGGGT | |||||||||
Keywords | DNA / DRUG-DNA COMPLEX / telomeric G-quadruplex | |||||||||
Function / homology | : / Chem-LKO / DNA / DNA (> 10) Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | |||||||||
Authors | Ferraroni, M. / Bazzicalupi, C. / Gratteri, P. / Papi, F. | |||||||||
Funding support | 2items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: Probing the Efficiency of 13-Pyridylalkyl Berberine Derivatives to Human Telomeric G-Quadruplexes Binding: Spectroscopic, Solid State and In Silico Analysis. Authors: Bazzicalupi, C. / Bonardi, A. / Biver, T. / Ferraroni, M. / Papi, F. / Savastano, M. / Lombardi, P. / Gratteri, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aad.cif.gz | 20.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aad.ent.gz | 11.3 KB | Display | PDB format |
PDBx/mmJSON format | 8aad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aad_validation.pdf.gz | 746.1 KB | Display | wwPDB validaton report |
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Full document | 8aad_full_validation.pdf.gz | 746.8 KB | Display | |
Data in XML | 8aad_validation.xml.gz | 3 KB | Display | |
Data in CIF | 8aad_validation.cif.gz | 3.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/8aad ftp://data.pdbj.org/pub/pdb/validation_reports/aa/8aad | HTTPS FTP |
-Related structure data
Related structure data | 7qvqC 7zurC 5cdbS C: citing same article (ref.) 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
#1: DNA chain | Mass: 3773.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-LKO / | #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: 1.9 Å3/Da / Density % sol: 56.4 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: NaCacodylate, NaI, MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97264 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97264 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.04→29.47 Å / Num. obs: 2137 / % possible obs: 99.8 % / Redundancy: 22.8 % / CC1/2: 1 / Net I/σ(I): 25.99 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CDB Resolution: 2.04→29.47 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.332 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.348 / ESU R Free: 0.255 / 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: 99.72 Å2 / Biso mean: 36.386 Å2 / Biso min: 8.46 Å2
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Refinement step | Cycle: final / Resolution: 2.04→29.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.045→2.098 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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