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- PDB-6cfo: HUMAN PYRUVATE DEHYDROGENASE E1 COMPONENT COMPLEX WITH COVALENT T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6cfo | ||||||
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Title | HUMAN PYRUVATE DEHYDROGENASE E1 COMPONENT COMPLEX WITH COVALENT TDP ADDUCT ACETYL PHOSPHINATE | ||||||
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![]() | OXIDOREDUCTASE / THIAMIN PYROPHOSPHATE / ACETYL PHOSPHINATE / INHIBITOR / PYRUVATE DEHYDROGENASE | ||||||
Function / homology | ![]() pyruvate dehydrogenase (NAD+) activity / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / acetyl-CoA biosynthetic process from pyruvate / : / pyruvate dehydrogenase complex / Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid ...pyruvate dehydrogenase (NAD+) activity / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / acetyl-CoA biosynthetic process from pyruvate / : / pyruvate dehydrogenase complex / Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / tricarboxylic acid cycle / Mitochondrial protein degradation / glucose metabolic process / mitochondrial matrix / nucleolus / mitochondrion / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | ARJUNAN, P. / WHITLEY, M.J. / FUREY, W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Pyruvate dehydrogenase complex deficiency is linked to regulatory loop disorder in the alpha V138M variant of human pyruvate dehydrogenase. Authors: Whitley, M.J. / Arjunan, P. / Nemeria, N.S. / Korotchkina, L.G. / Park, Y.H. / Patel, M.S. / Jordan, F. / Furey, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 543.4 KB | Display | ![]() |
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PDB format | ![]() | 444.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 51.3 KB | Display | |
Data in CIF | ![]() | 72.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6cerC ![]() 1ni4S 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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Unit cell |
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Components
#1: Protein | Mass: 40714.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P08559, pyruvate dehydrogenase (acetyl-transferring) #2: Protein | Mass: 37346.836 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P11177, pyruvate dehydrogenase (acetyl-transferring) #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 3350, SODIUM THIOCYANATE, MAGNESIUM CHLORIDE, THIAMIN PYROPHOSPHATE, ACETYL PHOSPHINATE, |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 14, 2009 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→47.575 Å / Num. obs: 44058 / % possible obs: 98.33 % / Observed criterion σ(I): 0 / Redundancy: 6.966 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.89 |
Reflection shell | Resolution: 2.7→2.86 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 5.28 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1NI4 Resolution: 2.7→47.575 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 26.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→47.575 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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