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- PDB-2gkd: Structural insight into self-sacrifice mechanism of enediyne resi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gkd | ||||||
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Title | Structural insight into self-sacrifice mechanism of enediyne resistance | ||||||
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![]() | TOXIN/DNA / START domain protein / TOXIN-DNA COMPLEX | ||||||
Function / homology | ![]() Activator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / simulated annealing, molecular dynamics, Docking | ||||||
![]() | Singh, S. / Thorson, J.S. | ||||||
![]() | ![]() Title: Structural insight into the self-sacrifice mechanism of enediyne resistance. Authors: Singh, S. / Hager, M.H. / Zhang, C. / Griffith, B.R. / Lee, M.S. / Hallenga, K. / Markley, J.L. / Thorson, J.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.9 KB | Display | ![]() |
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PDB format | ![]() | 61.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 248.5 KB | Display | ![]() |
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Full document | ![]() | 248.3 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 8.5 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: 3397.247 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3308.185 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 17915.072 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: ![]() |
NMR details | Text: NMR chemical shift perturbation information was used for docking. |
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Sample preparation
Details | Contents: U-15N, CalC, 50mM phosphate buffer, 150 mM NaCL / Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 150 mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing, molecular dynamics, Docking / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 1 |