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Yorodumi- PDB-8tbt: Structure of human erythrocyte pyruvate kinase in complex with an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tbt | ||||||
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Title | Structure of human erythrocyte pyruvate kinase in complex with an allosteric activator Compound 2 | ||||||
Components | Pyruvate kinase PKLR | ||||||
Keywords | TRANSFERASE/ACTIVATOR / Erythrocyte pyruvate kinase / PKR / PKLR / Allosteric Activator / Glycolysis / TRANSFERASE / TRANSFERASE-ACTIVATOR complex | ||||||
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 / response to metal ion / monosaccharide binding / 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 / response to metal ion / monosaccharide binding / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | ||||||
Authors | Jin, L. / Padyana, A. | ||||||
Funding support | 1items
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Citation | Journal: Chemmedchem / Year: 2024 Title: Structure-Based Design of AG-946, a Pyruvate Kinase Activator. Authors: Liu, T. / Padyana, A.K. / Judd, E.T. / Jin, L. / Hammoudeh, D. / Kung, C. / Dang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tbt.cif.gz | 495.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tbt.ent.gz | 326.3 KB | Display | PDB format |
PDBx/mmJSON format | 8tbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tbt_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 8tbt_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 8tbt_validation.xml.gz | 76.3 KB | Display | |
Data in CIF | 8tbt_validation.cif.gz | 104 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/8tbt ftp://data.pdbj.org/pub/pdb/validation_reports/tb/8tbt | HTTPS FTP |
-Related structure data
Related structure data | 8tbsC 8tbuC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 ABCD
#1: Protein | Mass: 58665.176 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Red blood cell/liver isoform / Source: (gene. exp.) Homo sapiens (human) / Gene: PKLR, PK1, PKL / Production host: Escherichia coli (E. coli) / References: UniProt: P30613, pyruvate kinase #2: Sugar | ChemComp-FBP / |
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-Non-polymers , 5 types, 375 molecules
#3: Chemical | ChemComp-PYR / #4: Chemical | ChemComp-MN / #5: Chemical | ChemComp-K / #6: Chemical | #7: 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: 2.47 Å3/Da / Density % sol: 50.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 10 mM MnSO4, 50 mM MES/KOH pH 6.0, 11 %(w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→33.77 Å / Num. obs: 92656 / % possible obs: 97.17 % / Redundancy: 3.7 % / Biso Wilson estimate: 45.28 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.342→2.426 Å / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 9114 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→33.77 Å / SU ML: 0.3151 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7819 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 56.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→33.77 Å
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Refine LS restraints |
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LS refinement shell |
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