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Yorodumi- PDB-2q8i: Pyruvate dehydrogenase kinase isoform 3 in complex with antitumor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q8i | ||||||
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Title | Pyruvate dehydrogenase kinase isoform 3 in complex with antitumor drug radicicol | ||||||
Components |
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Keywords | TRANSFERASE / GHKL ATPase/kinase family / pyruvate dehydrogenase complex / mitochondrial kinase / radicicol | ||||||
Function / homology | Function and homology information hypoxia-inducible factor-1alpha signaling pathway / [pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase (acetyl-transferring) kinase activity / pyruvate dehydrogenase complex / : / Pyruvate metabolism ...hypoxia-inducible factor-1alpha signaling pathway / [pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase (acetyl-transferring) kinase activity / pyruvate dehydrogenase complex / : / Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / regulation of reactive oxygen species metabolic process / cellular response to fatty acid / Signaling by Retinoic Acid / regulation of glucose metabolic process / tricarboxylic acid cycle / peroxisome proliferator activated receptor signaling pathway / cellular response to glucose stimulus / glucose metabolic process / peptidyl-serine phosphorylation / mitochondrial matrix / protein kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / nucleolus / mitochondrion / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å | ||||||
Authors | Kato, M. / Li, J. / Chuang, J.L. / Chuang, D.T. | ||||||
Citation | Journal: Structure / Year: 2007 Title: Distinct Structural Mechanisms for Inhibition of Pyruvate Dehydrogenase Kinase Isoforms by AZD7545, Dichloroacetate, and Radicicol. Authors: Kato, M. / Li, J. / Chuang, J.L. / Chuang, D.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q8i.cif.gz | 113.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q8i.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 2q8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/2q8i ftp://data.pdbj.org/pub/pdb/validation_reports/q8/2q8i | HTTPS FTP |
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-Related structure data
Related structure data | 2q8fSC 2q8gC 2q8hC 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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Details | The second part of the biological assembly is generated by the following operation, Y-X,Y,1/2-Z, of both the chain a and b. |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | [ Mass: 48290.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDK3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21 References: UniProt: Q15120, [pyruvate dehydrogenase (acetyl-transferring)] kinase |
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#2: Protein | Mass: 14192.097 Da / Num. of mol.: 1 / Fragment: lipoyl-bearing domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLAT, DLTA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P10515, dihydrolipoyllysine-residue acetyltransferase |
-Non-polymers , 5 types, 85 molecules
#3: Chemical | ChemComp-K / |
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#4: Chemical | ChemComp-RDC / |
#5: Chemical | ChemComp-GOL / |
#6: Chemical | ChemComp-RED / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.04 Å3/Da / Density % sol: 69.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: soudium citrate, sodium potassium phosphate, sodium chrolide, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: SBC-3 / Detector: CCD / Date: Oct 26, 2006 / Details: mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. obs: 32612 / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.054 / Χ2: 0.836 / Net I/σ(I): 10.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 2Q8F Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / SU B: 12.535 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.257 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.67 Å / Total num. of bins used: 20
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