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Open data
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Basic information
Entry | Database: PDB / ID: 8hmr | ||||||
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Title | Crystal Structure of PKM2 mutant L144P | ||||||
![]() | Pyruvate kinase PKM | ||||||
![]() | TRANSFERASE / PKM2 / Hydroxylation / Kinase / Glycolysis / Tumour Promoting / Warburg Effect | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Upadhyay, S. / Kumar, A. / Patel, A.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and mechanistic insights into cancer patient-derived mutations in Pyruvate Kinase muscle isoform 2 Authors: Upadhyay, S. / Kumar, A. / Patel, A.K. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 779.2 KB | Display | ![]() |
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PDB format | ![]() | 649.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 69.2 KB | Display | |
Data in CIF | ![]() | 93.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hmqC ![]() 8hmsC ![]() 8hmuC ![]() 3gr4S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein / Sugars , 2 types, 8 molecules ABCD![](data/chem/img/FBP.gif)
![](data/chem/img/FBP.gif)
#1: Protein | Mass: 60172.203 Da / Num. of mol.: 4 / Mutation: L144P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P14618, pyruvate kinase, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase #3: Sugar | ChemComp-FBP / |
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-Non-polymers , 4 types, 29 molecules ![](data/chem/img/OXL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-OXL / #4: Chemical | ChemComp-MG / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M Sodium chloride, 0.1 M HEPES pH7.0, 20% w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 24, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→44.16 Å / Num. obs: 63685 / % possible obs: 98 % / Redundancy: 4.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.054 / Rrim(I) all: 0.109 / Χ2: 1.03 / Net I/σ(I): 9 / Num. measured all: 261074 |
Reflection shell | Resolution: 2.6→2.66 Å / % possible obs: 100 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.847 / Num. measured all: 19161 / Num. unique obs: 4557 / CC1/2: 0.77 / Rpim(I) all: 0.469 / Rrim(I) all: 0.97 / Χ2: 0.9 / Net I/σ(I) obs: 1.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3GR4 Resolution: 2.6→42.01 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.914 / SU B: 56.658 / SU ML: 0.484 / Cross valid method: THROUGHOUT / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.345 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→42.01 Å
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