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Open data
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Basic information
Entry | Database: PDB / ID: 6gg5 | ||||||
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Title | Crystal structure of M2 PYK in complex with Tryptophan. | ||||||
![]() | Pyruvate kinase PKM | ||||||
![]() | TRANSFERASE / Glycolysis / Pyruvate Kinase Activity | ||||||
Function / homology | ![]() positive regulation of cytoplasmic translation / pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum ...positive regulation of cytoplasmic translation / pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / glycolytic process / non-specific protein-tyrosine kinase / cilium / cellular response to insulin stimulus / extracellular vesicle / MHC class II protein complex binding / protein tyrosine kinase activity / secretory granule lumen / collagen-containing extracellular matrix / vesicle / ficolin-1-rich granule lumen / transcription coactivator activity / non-specific serine/threonine protein kinase / cadherin binding / phosphorylation / mRNA binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / extracellular exosome / extracellular region / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McNae, I.W. / Yuan, M. / Walkinshaw, M.D. | ||||||
![]() | ![]() Title: An allostatic mechanism for M2 pyruvate kinase as an amino-acid sensor. Authors: Yuan, M. / McNae, I.W. / Chen, Y. / Blackburn, E.A. / Wear, M.A. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Hupp, T. / Walkinshaw, M.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 695.3 KB | Display | ![]() |
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PDB format | ![]() | 580.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 505.2 KB | Display | ![]() |
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Full document | ![]() | 518.4 KB | Display | |
Data in XML | ![]() | 60.8 KB | Display | |
Data in CIF | ![]() | 82.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gg3C ![]() 6gg4C ![]() 6gg6C ![]() 4fxjS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 60204.250 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-TRP / #4: Chemical | ChemComp-K / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.5 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 10-16% PEG 3350, 100 mM sodium Cacodylate, 50 mM MgCl2, 100 mM KCl PH range: 7.2-7.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9174 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→72.54 Å / Num. obs: 36606 / % possible obs: 98.2 % / Redundancy: 2.9 % / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 3.2→3.283 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4fxj Resolution: 3.2→72.54 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.847 / SU B: 68.313 / SU ML: 0.489 / Cross valid method: THROUGHOUT / ESU R Free: 0.563 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.959 Å2
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Refinement step | Cycle: 1 / Resolution: 3.2→72.54 Å
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Refine LS restraints |
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