+Open data
-Basic information
Entry | Database: PDB / ID: 6nub | ||||||
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Title | Pyruvate Kinase M2 Mutant - S437Y in Complex with L-serine | ||||||
Components | Pyruvate kinase PKM | ||||||
Keywords | TRANSFERASE / GLYCOLYSIS / GENE REGULATION / PHOSPHOTRANSFERASE / SERINE | ||||||
Function / homology | Function and homology information pyruvate kinase / pyruvate kinase activity / programmed cell death / Pyruvate metabolism / positive regulation of cytoplasmic translation / histone H3T11 kinase activity / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding ...pyruvate kinase / pyruvate kinase activity / programmed cell death / Pyruvate metabolism / positive regulation of cytoplasmic translation / histone H3T11 kinase activity / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / Regulation of pyruvate metabolism / glycolytic process / non-specific protein-tyrosine kinase / cellular response to insulin stimulus / cilium / extracellular vesicle / MHC class II protein complex binding / protein tyrosine kinase activity / secretory granule lumen / collagen-containing extracellular matrix / transcription coactivator activity / vesicle / ficolin-1-rich granule lumen / non-specific serine/threonine protein kinase / cadherin binding / mRNA binding / Neutrophil degranulation / magnesium ion binding / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / mitochondrion / RNA binding / extracellular exosome / extracellular region / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Srivastava, D. / Nandi, S. / Dey, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2019 Title: Mechanistic and Structural Insights into Cysteine-Mediated Inhibition of Pyruvate Kinase Muscle Isoform 2. Authors: Srivastava, D. / Nandi, S. / Dey, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nub.cif.gz | 245.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nub.ent.gz | 189.7 KB | Display | PDB format |
PDBx/mmJSON format | 6nub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nub_validation.pdf.gz | 1008.3 KB | Display | wwPDB validaton report |
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Full document | 6nub_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6nub_validation.xml.gz | 48.2 KB | Display | |
Data in CIF | 6nub_validation.cif.gz | 73 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/6nub ftp://data.pdbj.org/pub/pdb/validation_reports/nu/6nub | HTTPS FTP |
-Related structure data
Related structure data | 6nu1C 6nu5C 6b6uS 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60126.195 Da / Num. of mol.: 2 / Mutation: S437Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PKM, OIP3, PK2, PK3, PKM2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P14618, pyruvate kinase |
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-Non-polymers , 10 types, 1035 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SCN / #7: Chemical | ChemComp-PEG / | #8: Chemical | #9: Chemical | ChemComp-PG4 / | #10: Chemical | ChemComp-EDO / | #11: 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: 2.41 Å3/Da / Density % sol: 48.87 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M SODIUM THIOCYANATE, 100 mM BIS-TRIS PROPANE, 16-20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Sep 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→41.96 Å / Num. obs: 121214 / % possible obs: 99.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 17221 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6B6U Resolution: 1.7→36.806 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→36.806 Å
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Refine LS restraints |
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LS refinement shell |
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