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Open data
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Basic information
Entry | Database: PDB / ID: 6nn7 | ||||||||||||||||||
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Title | The structure of human liver pyruvate kinase, hLPYK-GGG | ||||||||||||||||||
![]() | Pyruvate kinase PKLR | ||||||||||||||||||
![]() | TRANSFERASE / pyruvate kinase / allosteric / glycolysis | ||||||||||||||||||
Function / homology | ![]() pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / response to metal ion / monosaccharide binding / Glycolysis / response to ATP ...pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / response to metal ion / monosaccharide binding / Glycolysis / response to ATP / potassium ion binding / Regulation of gene expression in beta cells / response to glucose / response to cAMP / cellular response to epinephrine stimulus / response to nutrient / glycolytic process / cellular response to insulin stimulus / kinase activity / response to hypoxia / phosphorylation / magnesium ion binding / extracellular exosome / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | McFarlane, J.S. / Ronnebaum, T.A. / Meneely, K.M. / Fenton, A.W. / Lamb, A.L. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Changes in the allosteric site of human liver pyruvate kinase upon activator binding include the breakage of an intersubunit cation-pi bond. Authors: McFarlane, J.S. / Ronnebaum, T.A. / Meneely, K.M. / Chilton, A. / Fenton, A.W. / Lamb, A.L. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 570.6 KB | Display | ![]() |
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Full document | ![]() | 628.9 KB | Display | |
Data in XML | ![]() | 128.5 KB | Display | |
Data in CIF | ![]() | 175.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nn4C ![]() 6nn5C ![]() 6nn8C ![]() 4ip7S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 58437.020 Da / Num. of mol.: 8 / Fragment: UNP residues 34-574 / Mutation: Del529, S531G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.91 % Description: Crystals grew as rectangular prisms within two days and reached full size within two weeks. |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2 M ammonium citrate, pH 6.0, 24% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2017 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→39.06 Å / Num. obs: 175876 / % possible obs: 89.4 % / Redundancy: 3.9 % / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.32→2.36 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4IP7 Resolution: 2.32→39.06 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.07
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→39.06 Å
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Refine LS restraints |
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LS refinement shell |
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