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Yorodumi- PDB-6tmp: Rapid optimisation of fragments and hits to lead compounds from s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tmp | ||||||
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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 / Regulation of pyruvate dehydrogenase (PDH) complex / pyruvate dehydrogenase complex / regulation of cellular ketone metabolic process / regulation of pH / cellular response to nutrient / Signaling by Retinoic Acid / regulation of gluconeogenesis ...[pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase (acetyl-transferring) kinase activity / Regulation of pyruvate dehydrogenase (PDH) complex / pyruvate dehydrogenase complex / regulation of cellular ketone metabolic process / regulation of pH / cellular response to nutrient / 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 / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.076 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 | 6tmp.cif.gz | 147.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tmp.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6tmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/6tmp ftp://data.pdbj.org/pub/pdb/validation_reports/tm/6tmp | HTTPS FTP |
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-Related structure data
Related structure data | 6tmqC 6tmzC 6tn0C 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 on special symmetry positions |
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-Components
#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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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-NN8 / [ |
#4: Chemical | ChemComp-TF3 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-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: 61.92 % |
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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: 2.076→94.65 Å / Num. obs: 19985 / % possible obs: 93.9 % / Redundancy: 10.2 % / CC1/2: 1 / Rmerge(I) obs: 0.092 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.076→2.344 Å / Redundancy: 9.2 % / Rmerge(I) obs: 1.197 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1000 / CC1/2: 0.747 / % possible all: 76.2 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.076→94.65 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.922 / Cross valid method: FREE R-VALUE / ESU R: 0.281 / ESU R Free: 0.24 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: 47.262 Å2
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Refinement step | Cycle: LAST / Resolution: 2.076→94.65 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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