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- PDB-6nn4: The structure of human liver pyruvate kinase, hLPYK-D499N, in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nn4 | ||||||||||||||||||
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Title | The structure of human liver pyruvate kinase, hLPYK-D499N, in complex with Fru-1,6-BP | ||||||||||||||||||
![]() | 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 | ![]() | 616.6 KB | Display | ![]() |
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PDB format | ![]() | 511.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 62.6 KB | Display | |
Data in CIF | ![]() | 86.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nn5C ![]() 6nn7C ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 58563.176 Da / Num. of mol.: 4 / Fragment: UNP residues 34-574 / Mutation: D499N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | ChemComp-FBP / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEP / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.42 % 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 / Details: 0.2 M ammonium citrate dibasic, 20% 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: Jan 28, 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: 2.15→39.44 Å / Num. obs: 149968 / % possible obs: 99 % / Redundancy: 4.2 % / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.15→2.19 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4IP7 Resolution: 2.15→39.437 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→39.437 Å
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Refine LS restraints |
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LS refinement shell |
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