+Open data
-Basic information
Entry | Database: PDB / ID: 2kar | ||||||
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Title | HNE-dG adduct mismatched with dA in acidic solution | ||||||
Components |
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Keywords | DNA / HNE-dG / mismatch / hydroxynonenal | ||||||
Function / homology | (4S)-nonane-1,4-diol / DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Huang, H. / Wang, H. / Lloyd, R.S. / Rizzo, C.J. / Stone, M.P. | ||||||
Citation | Journal: Chem.Res.Toxicol. / Year: 2009 Title: Conformational interconversion of the trans-4-hydroxynonenal-derived (6S,8R,11S) 1,N(2)-deoxyguanosine adduct when mismatched with deoxyadenosine in DNA Authors: Huang, H. / Wang, H. / Lloyd, R.S. / Rizzo, C.J. / Stone, M.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kar.cif.gz | 27.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kar.ent.gz | 17 KB | Display | PDB format |
PDBx/mmJSON format | 2kar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kar_validation.pdf.gz | 307.2 KB | Display | wwPDB validaton report |
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Full document | 2kar_full_validation.pdf.gz | 307 KB | Display | |
Data in XML | 2kar_validation.xml.gz | 3.1 KB | Display | |
Data in CIF | 2kar_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/2kar ftp://data.pdbj.org/pub/pdb/validation_reports/ka/2kar | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The DNA oligomer is chemically synthesized. |
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#2: DNA chain | Mass: 3687.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The DNA oligomer is chemically synthesized. |
#3: Chemical | ChemComp-HND / ( |
Nonpolymer details | THE LIGAND HND FORMS TWO COVALENT BONDS WITH THE DEOXY-GUANINE AT POSITION 7 OF CHAIN A. THIS ...THE LIGAND HND FORMS TWO COVALENT BONDS WITH THE DEOXY-GUANINE AT POSITION 7 OF CHAIN A. THIS LIGAND IS FORMED BY CHEMICAL REACTION OF ANOTHER LIGAND HNE |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D 1H-1H NOESY |
-Sample preparation
Details | Contents: 1.0 mM DNA 5'-D(*DGP*DCP*DTP*DAP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DC)-3', 1.0 mM 5'-D(*DGP*DGP*DAP*DCP*DTP*DAP*DGP*DCP*DTP*DAP*DGP*DC)-3', 1.0 mM (2E,4R)-4-HYDROXYNON-2-ENAL, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 100 / pH: 5.5 / Pressure: ambient / Temperature: 288 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software | Name: Amber Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 |
NMR representative | Selection criteria: closest to the average |
NMR ensemble | Conformer selection criteria: back calculated data agree with experimental NOESY spectrum Conformers calculated total number: 10 / Conformers submitted total number: 1 |