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- PDB-6wkz: Cocomplex structure of Deoxyhypusine synthase with inhibitor 6-[(... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wkz | ||||||
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Title | Cocomplex structure of Deoxyhypusine synthase with inhibitor 6-[(1R)-2-AMINO-1-PHENYLETHYL]-3-(PYRIDIN-3-YL)-4H,5H,6H,7H-THIENO[2,3-C]PYRIDIN-7-ONE | ||||||
![]() | Deoxyhypusine synthase | ||||||
![]() | TRANSFERASE/INHIBITOR / Deoxyhypusine / Inhibitor / Transferase / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | ![]() deoxyhypusine synthase / Hypusine synthesis from eIF5A-lysine / peptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase activity / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation ...deoxyhypusine synthase / Hypusine synthesis from eIF5A-lysine / peptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase activity / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Klein, M.G. / Ambrus-Aikelin, G. | ||||||
![]() | ![]() Title: New Series of Potent Allosteric Inhibitors of Deoxyhypusine Synthase. Authors: Tanaka, Y. / Kurasawa, O. / Yokota, A. / Klein, M.G. / Saito, B. / Matsumoto, S. / Okaniwa, M. / Ambrus-Aikelin, G. / Uchiyama, N. / Morishita, D. / Kimura, H. / Imamura, 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 | ![]() | 250.5 KB | Display | ![]() |
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PDB format | ![]() | 201.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 31.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wl6C ![]() 6p4vS ![]() 5v15 ![]() 5v2e S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41213.613 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 100mM Hepes (pH 7.0) and 2M sodium/potassium phosphate (pH 5.0) |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→50 Å / Num. obs: 50674 / % possible obs: 100 % / Redundancy: 4.8 % / Rsym value: 0.091 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.23→2.27 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2807 / Rsym value: 0.955 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6P4V Resolution: 2.23→37.36 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 10.176 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.004 Å2
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Refinement step | Cycle: 1 / Resolution: 2.23→37.36 Å
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Refine LS restraints |
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