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Yorodumi- PDB-6tn0: Rapid optimisation of fragments and hits to lead compounds from s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tn0 | ||||||
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Title | Rapid optimisation of fragments and hits to lead compounds from screening of crude reaction mixtures | ||||||
Components | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | ||||||
Keywords | TRANSFERASE / OFF-RATE SCREENING / PDHK / HSP90 / SPR / KINASE INHIBITORS / FRAGMENT SCREENING / CANCER / PDK1 / PDK2 / PDK3 / PDK4 | ||||||
Function / homology | Function and homology information [pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase (acetyl-transferring) kinase activity / : / pyruvate dehydrogenase complex / regulation of cellular ketone metabolic process / regulation of pH / cellular response to nutrient / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid ...[pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase (acetyl-transferring) kinase activity / : / pyruvate dehydrogenase complex / regulation of cellular ketone metabolic process / regulation of pH / cellular response to nutrient / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / regulation of gluconeogenesis / intrinsic apoptotic signaling pathway by p53 class mediator / regulation of glucose metabolic process / regulation of calcium-mediated signaling / cellular response to reactive oxygen species / glucose metabolic process / insulin receptor signaling pathway / glucose homeostasis / protein kinase activity / mitochondrial matrix / phosphorylation / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.905 Å | ||||||
Authors | Baker, L.M. / Aimon, A. / Murray, J.B. / Surgenor, A.E. / Matassova, N. / Roughley, S.D. / von Delft, F. / Hubbard, R.E. | ||||||
Citation | Journal: Commun Chem / Year: 2020 Title: Rapid optimisation of fragments and hits to lead compounds from screening of crude reaction mixtures Authors: Baker, L.M. / Aimon, A. / Murray, J.B. / Surgenor, A.E. / Matassova, N. / Roughley, S.D. / Collins, P.M. / Krojer, T. / von Delft, F. / Hubbard, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tn0.cif.gz | 145.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tn0.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6tn0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tn0_validation.pdf.gz | 902.9 KB | Display | wwPDB validaton report |
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Full document | 6tn0_full_validation.pdf.gz | 904.7 KB | Display | |
Data in XML | 6tn0_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 6tn0_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/6tn0 ftp://data.pdbj.org/pub/pdb/validation_reports/tn/6tn0 | HTTPS FTP |
-Related structure data
Related structure data | 6tmpC 6tmqC 6tmzC 6tn2C 6tn4C 6tn5C 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
-Protein , 1 types, 1 molecules AAA
#1: Protein | [ Mass: 44647.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDK2, PDHK2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS References: UniProt: Q15119, [pyruvate dehydrogenase (acetyl-transferring)] kinase |
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-Non-polymers , 5 types, 150 molecules
#2: Chemical | ChemComp-TF3 / |
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#3: Chemical | ChemComp-NLZ / |
#4: Chemical | ChemComp-DMS / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Details
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: 3.23 Å3/Da / Density % sol: 61.89 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 0.1 M Sodium acetate pH 5.8 0.125 M Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 1.905→94.441 Å / Num. obs: 27801 / % possible obs: 94.3 % / Redundancy: 10.3 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 1.905→2.13 Å / Rmerge(I) obs: 1.241 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1390 / CC1/2: 0.713 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.905→94.441 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: FREE R-VALUE / ESU R: 0.176 / ESU R Free: 0.166 Details: Hydrogens have been added in their 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: 46.489 Å2
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Refinement step | Cycle: LAST / Resolution: 1.905→94.441 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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