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Open data
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Basic information
Entry | Database: PDB / ID: 1y8p | ||||||
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Title | Crystal structure of the PDK3-L2 complex | ||||||
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Function / homology | ![]() hypoxia-inducible factor-1alpha signaling pathway / [pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kato, M. / Chuang, J.L. / Wynn, R.M. / Chuang, D.T. | ||||||
![]() | ![]() Title: Crystal structure of pyruvate dehydrogenase kinase 3 bound to lipoyl domain 2 of human pyruvate dehydrogenase complex. Authors: Kato, M. / Chuang, J.L. / Tso, S.C. / Wynn, R.M. / Chuang, D.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 | ![]() | 115.8 KB | Display | ![]() |
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PDB format | ![]() | 86.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1y8nC ![]() 1y8oC ![]() 1jm6S 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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Details | The second part of the biological assembly is generated by the operation: y-x-1, y, 1/2-z. |
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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.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 14192.097 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P10515, ![]() |
-Non-polymers , 5 types, 61 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/RED.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/RED.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-ATP / | ![]() #6: Chemical | ChemComp-RED / | ![]() #7: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.7 Å3/Da / Density % sol: 73.7 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 310 / Detector: CCD / Date: Aug 17, 2003 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.62→50 Å / Num. all: 31538 / Num. obs: 31043 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.62→2.71 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2970 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDK2 PDB entry 1JM6 Resolution: 2.63→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 14.983 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.295 / ESU R Free: 0.227 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.251 Å2
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Refine analyze | Luzzati coordinate error obs: 0.457 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.63→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.63→2.699 Å / Total num. of bins used: 20
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