+Open data
-Basic information
Entry | Database: PDB / ID: 6nn8 | ||||||||||||||||||
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Title | The structure of human liver pyruvate kinase, hLPYK-S531E | ||||||||||||||||||
Components | Pyruvate kinase PKLR | ||||||||||||||||||
Keywords | TRANSFERASE / pyruvate kinase / allosteric / glycolysis | ||||||||||||||||||
Function / homology | Function and homology information pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / monosaccharide binding / response to metal ion / 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 / monosaccharide binding / response to metal ion / 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 / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.416 Å | ||||||||||||||||||
Authors | McFarlane, J.S. / Ronnebaum, T.A. / Meneely, K.M. / Fenton, A.W. / Lamb, A.L. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nn8.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6nn8.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 6nn8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/6nn8 ftp://data.pdbj.org/pub/pdb/validation_reports/nn/6nn8 | HTTPS FTP |
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-Related structure data
Related structure data | 6nn4C 6nn5C 6nn7C 4ip7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 58606.199 Da / Num. of mol.: 8 / Fragment: UNP residues 34-574 / Mutation: S531E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PKLR, PK1, PKL / Production host: Escherichia coli (E. coli) / References: UniProt: P30613, pyruvate kinase #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.58 % 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, pH 5.6, 16% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2018 |
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: 2.416→39.538 Å / Num. obs: 173222 / % possible obs: 98.9 % / Redundancy: 7 % / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.416→2.46 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4IP7 Resolution: 2.416→39.538 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.416→39.538 Å
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Refine LS restraints |
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LS refinement shell |
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