+Open data
-Basic information
Entry | Database: PDB / ID: 6v76 | ||||||
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Title | Crystal Structure of Human PKM2 in Complex with L-valine | ||||||
Components | Pyruvate kinase PKM | ||||||
Keywords | TRANSFERASE / glycolytic enzyme / tetramer / amino acid binding | ||||||
Function / homology | Function and homology information programmed cell death / pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / histone H3T11 kinase activity / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum ...programmed cell death / pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / histone H3T11 kinase activity / 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 / collagen-containing extracellular matrix / protein tyrosine kinase activity / secretory granule lumen / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Nandi, S. / Dey, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Biochemical and structural insights into how amino acids regulate pyruvate kinase muscle isoform 2. Authors: 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 | 6v76.cif.gz | 366.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v76.ent.gz | 287.8 KB | Display | PDB format |
PDBx/mmJSON format | 6v76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/6v76 ftp://data.pdbj.org/pub/pdb/validation_reports/v7/6v76 | HTTPS FTP |
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-Related structure data
Related structure data | 6v74C 6v75C 6nu1S 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 / Sugars , 2 types, 8 molecules CABD
#1: Protein | Mass: 60050.102 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PKM, OIP3, PK2, PK3, PKM2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14618, pyruvate kinase #5: Sugar | ChemComp-FBP / |
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-Non-polymers , 7 types, 85 molecules
#2: Chemical | #3: Chemical | ChemComp-K / | #4: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.35 Å3/Da / Density % sol: 47.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M NaBr, 0.1 M Bis-Tris propane, 24% 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: Nov 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: 2.75→77.718 Å / Num. all: 57593 / Num. obs: 57593 / % possible obs: 100 % / Redundancy: 7.2 % / Rpim(I) all: 0.036 / Rrim(I) all: 0.098 / Rsym value: 0.083 / Net I/av σ(I): 8.7 / Net I/σ(I): 17.3 / Num. measured all: 416317 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NU1 Resolution: 2.75→61.44 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.66 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.65 Å2 / Biso mean: 54.1293 Å2 / Biso min: 25.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→61.44 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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