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Yorodumi- PDB-6wkz: Cocomplex structure of Deoxyhypusine synthase with inhibitor 6-[(... -
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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 | ||||||
Components | Deoxyhypusine synthase | ||||||
Keywords | TRANSFERASE/INHIBITOR / Deoxyhypusine / Inhibitor / Transferase / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information deoxyhypusine synthase / deoxyhypusine synthase activity / Hypusine synthesis from eIF5A-lysine / peptidyl-lysine modification to peptidyl-hypusine / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation ...deoxyhypusine synthase / deoxyhypusine synthase activity / Hypusine synthesis from eIF5A-lysine / peptidyl-lysine modification to peptidyl-hypusine / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å | ||||||
Authors | Klein, M.G. / Ambrus-Aikelin, G. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wkz.cif.gz | 250.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wkz.ent.gz | 201.6 KB | Display | PDB format |
PDBx/mmJSON format | 6wkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/6wkz ftp://data.pdbj.org/pub/pdb/validation_reports/wk/6wkz | HTTPS FTP |
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-Related structure data
Related structure data | 6wl6C 6p4vS 5v15 5v2e S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: DHPS, DS / Production host: Escherichia coli (E. coli) / References: UniProt: P49366, deoxyhypusine synthase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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