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Yorodumi- PDB-5odf: NtMe polyamide in complex with 5'CGATGTACATCG3'- hairpin polyamid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5odf | ||||||||||||||||||||
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Title | NtMe polyamide in complex with 5'CGATGTACATCG3'- hairpin polyamides studies | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA BINDING PROTEIN / DNA / Minor groove binders / Hairpin polyamides | Function / homology | NtMe polyamide / DNA / DNA (> 10) | Function and homology information Biological species | Homo sapiens (human) | Method | SOLUTION NMR / molecular dynamics | Authors | Padroni, G. / Parkinson, J. / Burley, G.A. | Citation | Journal: Nucleic Acids Res. / Year: 2018 | Title: Structural basis of DNA duplex distortion induced by thiazole-containing hairpin polyamides. Authors: Padroni, G. / Parkinson, J.A. / Fox, K.R. / Burley, G.A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5odf.cif.gz | 190.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5odf.ent.gz | 154.4 KB | Display | PDB format |
PDBx/mmJSON format | 5odf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5odf_validation.pdf.gz | 533 KB | Display | wwPDB validaton report |
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Full document | 5odf_full_validation.pdf.gz | 730.5 KB | Display | |
Data in XML | 5odf_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 5odf_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/5odf ftp://data.pdbj.org/pub/pdb/validation_reports/od/5odf | HTTPS FTP |
-Related structure data
Related structure data | 5oczC 5odmC 5oe1C C: citing same article (ref.) |
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Similar structure data | |
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: 3582.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #2: Chemical | ChemComp-CWN / | |
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-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 | Ionic strength: 100 Phosphate mM / Label: NtMe PA / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 3 | ||||||||||||||||||
NMR representative | Selection criteria: na | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: na / Conformers calculated total number: 10 / Conformers submitted total number: 10 |