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Yorodumi- PDB-9f3d: Single acyclic phosphonate nucleotide (S)-ZNA modification on DNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9f3d | ||||||
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Title | Single acyclic phosphonate nucleotide (S)-ZNA modification on DNA hairpin | ||||||
Components | C modifed (S)-ZNA | ||||||
Keywords | DNA / XNA / Dickerson Drew Decamers / (S)-ZNA / acyclic backbone / phosphonate linkage | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Li, X. / Groaz, E. / Herdewijn, P. / Lescrinier, E. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Chemistry / Year: 2024 Title: Impact of Single Acyclic Phosphonate Nucleotide (ZNA) Modifications on DNA Duplex Stability. Authors: Li, X. / Groaz, E. / Herdewijn, P. / Lescrinier, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9f3d.cif.gz | 144.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9f3d.ent.gz | 91.9 KB | Display | PDB format |
PDBx/mmJSON format | 9f3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9f3d_validation.pdf.gz | 395.4 KB | Display | wwPDB validaton report |
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Full document | 9f3d_full_validation.pdf.gz | 479.3 KB | Display | |
Data in XML | 9f3d_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 9f3d_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/9f3d ftp://data.pdbj.org/pub/pdb/validation_reports/f3/9f3d | HTTPS FTP |
-Related structure data
Related structure data | 9f3eC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
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: 3635.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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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: torsion angle dynamics / Software ordinal: 3 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry Conformers calculated total number: 100 / Conformers submitted total number: 20 |