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Yorodumi- PDB-7msv: Solution Structure of Berberine Bound to a dGMP Fill-in G-Quadrup... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7msv | ||||||||||||||||||||||||||||
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Title | Solution Structure of Berberine Bound to a dGMP Fill-in G-Quadruplex in the PDGFR-b Promoter | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / G-quadruplex / promoter / Guanine metabolite | Function / homology | BERBERINE / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / DNA / DNA (> 10) | Function and homology information Biological species | Homo sapiens (human) | Method | SOLUTION NMR / molecular dynamics | Authors | Wang, K.B. / Dickerhoff, J. / Yang, D. | Funding support | United States, 1items |
Citation | Journal: J.Am.Chem.Soc. / Year: 2021 | Title: Solution Structure of Ternary Complex of Berberine Bound to a dGMP-Fill-In Vacancy G-Quadruplex Formed in the PDGFR-beta Promoter. Authors: Wang, K.B. / Dickerhoff, J. / Yang, D. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7msv.cif.gz | 147.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7msv.ent.gz | 121.2 KB | Display | PDB format |
PDBx/mmJSON format | 7msv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7msv_validation.pdf.gz | 492.2 KB | Display | wwPDB validaton report |
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Full document | 7msv_full_validation.pdf.gz | 540.5 KB | Display | |
Data in XML | 7msv_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 7msv_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/7msv ftp://data.pdbj.org/pub/pdb/validation_reports/ms/7msv | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 6009.886 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||
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#2: Chemical | ChemComp-DGP / | ||
#3: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 4 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |