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- PDB-1eki: AVERAGE SOLUTION STRUCTURE OF D(TTGGCCAA)2 BOUND TO CHROMOMYCIN-A... -
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Basic information
Entry | Database: PDB / ID: 1eki | |||||||||||||||||||||||
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Title | AVERAGE SOLUTION STRUCTURE OF D(TTGGCCAA)2 BOUND TO CHROMOMYCIN-A3 AND COBALT | |||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / drug bound in the minor groove of DNA | Function / homology | : / Chem-CPH / DNA | ![]() Method | SOLUTION NMR / simulated annealing | Model type details | minimized average | ![]() Gochin, M. | ![]() ![]() Title: A high-resolution structure of a DNA-chromomycin-Co(II) complex determined from pseudocontact shifts in nuclear magnetic resonance. Authors: Gochin, M. #1: ![]() Title: Structure determination by restrained molecular dynamics using NMR pseudocontact shifts as experimentally determined constraints Authors: Tu, K. / Gochin, M. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 31.4 KB | Display | ![]() |
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PDB format | ![]() | 21.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 648.3 KB | Display | ![]() |
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Full document | ![]() | 656.1 KB | Display | |
Data in XML | ![]() | 4.5 KB | Display | |
Data in CIF | ![]() | 5.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: TWO MOLECULES OF THE DRUG CHROMOMYCIN A3 (1GL-2GL-DXB-DDA-DDA-1AR, CHAINS C, AND D) ARE BOUND IN THE MINOR GROOVE #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-CO / | #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques as well as 2D 13C-1H heteronuclear correlation |
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Sample preparation
Details | Contents: 2mM DNA-drug complex, 25 degrees C, in buffer (100mM NaCl, 10mM Na borate), final PH 6. Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 110mM / pH: 6 / Pressure: 1 atm / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: GE OMEGA / Manufacturer: GE / Model: OMEGA / Field strength: 500 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: molecular dynamics, isolated spin-pair approximation for NOE's; pseudocontact shift refinement | ||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: average structure / Conformers calculated total number: 1 / Conformers submitted total number: 1 |