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- PDB-7ebh: Crystal structure of human pyruvate dehydrogenase kinase 2 in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ebh | ||||||
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Title | Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 13 | ||||||
![]() | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | ||||||
![]() | TRANSFERASE / PDHK / KINASE INHIBITORS / FRAGMENT SCREENING / PDK1 / PDK2 / PDK3 / PDK4 | ||||||
Function / homology | ![]() [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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Orita, T. / Doi, S. / Iwanaga, T. / Adachi, T. | ||||||
![]() | ![]() Title: Fragment-based lead discovery to identify novel inhibitors that target the ATP binding site of pyruvate dehydrogenase kinases. Authors: Akaki, T. / Bessho, Y. / Ito, T. / Fujioka, S. / Ubukata, M. / Mori, G. / Yamanaka, K. / Orita, T. / Doi, S. / Iwanaga, T. / Ikegashira, K. / Hantani, Y. / Nakanishi, I. / Adachi, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 178.1 KB | Display | ![]() |
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PDB format | ![]() | 125.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 729.9 KB | Display | ![]() |
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Full document | ![]() | 730.6 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ea0C ![]() 7easC ![]() 7eatC ![]() 7ebbC ![]() 7ebgC ![]() 2btzS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | [ Mass: 44647.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q15119, [pyruvate dehydrogenase (acetyl-transferring)] kinase |
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-Non-polymers , 5 types, 94 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/J0F.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/J0F.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-J0F / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.19 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 50 mM Na acetate pH 5.5, 100 mM magnesium chloride and 8% (v/v) isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→94.7 Å / Num. obs: 40300 / % possible obs: 98.7 % / Redundancy: 10.1 % / Biso Wilson estimate: 41.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.018 / Rrim(I) all: 0.059 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.96→2.02 Å / Redundancy: 10 % / Rmerge(I) obs: 1.015 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2943 / CC1/2: 0.802 / Rpim(I) all: 0.333 / Rrim(I) all: 1.069 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2btz Resolution: 1.96→94.7 Å / SU ML: 0.2166 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5776 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→94.7 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 46.7495288993 Å / Origin y: 45.6732922148 Å / Origin z: 72.4035994514 Å
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Refinement TLS group | Selection details: all |