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- PDB-2kv6: Tetrapeptide KWKK conjugated to oligonucleotide duplex by a trime... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2kv6 | ||||||
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Title | Tetrapeptide KWKK conjugated to oligonucleotide duplex by a trimethylene tether | ||||||
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![]() | DNA BINDING PROTEIN/DNA / DNA-peptide conjugate / trimethylene / acrolein-dG adduct / DNA-peptide complex / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | closest to the average, model 1 | ||||||
![]() | Huang, H. / Kozekov, I.D. / Kozekova, A. / Rizzo, C.J. / McCullough, A. / LLoyd, R.S. / Stone, M.P. | ||||||
![]() | ![]() Title: Minor Groove Orientation of the KWKK Peptide Tethered via the N-Terminal Amine to the Acrolein-Derived 1,N(2)-gamma-Hydroxypropanodeoxyguanosine Lesion with a Trimethylene Linkage . Authors: Huang, H. / Kozekov, I.D. / Kozekova, A. / Rizzo, C.J. / McCullough, A.K. / Lloyd, R.S. / Stone, M.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 24.6 KB | Display | ![]() |
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PDB format | ![]() | 17.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 335.6 KB | Display | ![]() |
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Full document | ![]() | 340 KB | Display | |
Data in XML | ![]() | 2.5 KB | Display | |
Data in CIF | ![]() | 2.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 3705.472 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3663.392 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein/peptide | Mass: 591.764 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 0.8 mM DNA (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3')-1, 0.8 mM DNA (5'-D(*GP*GP*AP*CP*TP*CP*GP*CP*TP*AP*GP*C)-3')-2, 0.8 mM entity_3-3, 100% D2O Solvent system: 100% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 100 / pH: 5.3 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 800 MHz |
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Processing
NMR software | Name: ![]() 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 |