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Yorodumi- PDB-6b2q: Dual Inhibition of the Essential Protein Kinases A and B in Mycob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b2q | ||||||
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Title | Dual Inhibition of the Essential Protein Kinases A and B in Mycobacterium tuberculosis | ||||||
Components | Serine/threonine-protein kinase PknA | ||||||
Keywords | TRANSFERASE/INHIBITOR / kinase / drug design / tuberculosis / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information peptidyl-threonine autophosphorylation / protein serine/threonine kinase activity => GO:0004674 / negative regulation of lipid biosynthetic process / negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / positive regulation of catalytic activity / positive regulation of DNA binding / regulation of cell shape / protein autophosphorylation / membrane => GO:0016020 ...peptidyl-threonine autophosphorylation / protein serine/threonine kinase activity => GO:0004674 / negative regulation of lipid biosynthetic process / negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / positive regulation of catalytic activity / positive regulation of DNA binding / regulation of cell shape / protein autophosphorylation / membrane => GO:0016020 / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / extracellular region / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.88 Å | ||||||
Authors | Zuccola, H.J. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2017 Title: Mtb PKNA/PKNB Dual Inhibition Provides Selectivity Advantages for Inhibitor Design To Minimize Host Kinase Interactions. Authors: Wang, T. / Bemis, G. / Hanzelka, B. / Zuccola, H. / Wynn, M. / Moody, C.S. / Green, J. / Locher, C. / Liu, A. / Gao, H. / Xu, Y. / Wang, S. / Wang, J. / Bennani, Y.L. / Thomson, J.A. / Muh, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b2q.cif.gz | 420 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b2q.ent.gz | 360.2 KB | Display | PDB format |
PDBx/mmJSON format | 6b2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/6b2q ftp://data.pdbj.org/pub/pdb/validation_reports/b2/6b2q | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34016.840 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pknA / Production host: Escherichia coli (E. coli) References: UniProt: A5TY85, UniProt: P9WI83*PLUS, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-CJJ / #3: Sugar | ChemComp-0BD / | |
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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: 2.62 Å3/Da / Density % sol: 53.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 3M sodium formate, 0.1 M buffer (ADA, cacodylate, or sodium citrate) pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.548→158 Å / Num. obs: 38607 / % possible obs: 89 % / Redundancy: 5.8 % / Biso Wilson estimate: 89.05 Å2 / Net I/σ(I): 15.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.88→113.72 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.898 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.383
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Displacement parameters | Biso mean: 90.01 Å2
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Refine analyze | Luzzati coordinate error obs: 0.43 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.88→113.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.88→2.97 Å / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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