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- PDB-2bu8: crystal structures of human pyruvate dehydrogenase kinase 2 conta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bu8 | ||||||
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Title | crystal structures of human pyruvate dehydrogenase kinase 2 containing physiological and synthetic ligands | ||||||
![]() | PYRUVATE DEHYDROGENASE KINASE ISOENZYME 2 | ||||||
![]() | TRANSFERASE / PYRUVATE DEHYDROGENASE KINASE 2 GHKL MOTIF REGULATION | ||||||
Function / homology | ![]() [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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Knoechel, T.R. / Tucker, A.D. / Robinson, C.M. / Phillips, C. / Taylor, W. / Bungay, P.J. / Kasten, S.A. / Roche, T.E. / Brown, D.G. | ||||||
![]() | ![]() Title: Regulatory Roles of the N-Terminal Domain Based on Crystal Structures of Human Pyruvate Dehydrogenase Kinase 2 Containing Physiological and Synthetic Ligands. Authors: Knoechel, T.R. / Tucker, A.D. / Robinson, C.M. / Phillips, C. / Taylor, W. / Bungay, P.J. / Kasten, S.A. / Roche, T.E. / Brown, D.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.3 KB | Display | ![]() |
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PDB format | ![]() | 67.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2btzSC ![]() 2bu2C ![]() 2bu5C ![]() 2bu6C ![]() 2bu7C S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 44647.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-TF4 / |
#5: Water | ChemComp-HOH / |
Sequence details | N -TERMINAL GS CLONING ARTEFACT |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100MM MES PH5.8-6,10% ISOPROPANOL,200MM CALCIUM ACETATE,10MG/ML PROTEIN,4 DEGREES, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 21614 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.23 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BTZ Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: BABINET / Bsol: 73.5571 Å2 / ksol: 0.355715 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Xplor file |
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