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Yorodumi- PDB-6b2p: Dual Inhibition of the Essential Protein Kinases A and B in Mycob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b2p | ||||||
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Title | Dual Inhibition of the Essential Protein Kinases A and B in Mycobacterium tuberculosis | ||||||
Components | Serine/threonine-protein kinase PknB | ||||||
Keywords | TRANSFERASE/INHIBITOR / kinase / drug design / tuberculosis / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information negative regulation of growth rate / protein serine/threonine kinase activity => GO:0004674 / acetyltransferase activator activity / negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / response to host immune response / positive regulation of catalytic activity / positive regulation of DNA binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall ...negative regulation of growth rate / protein serine/threonine kinase activity => GO:0004674 / acetyltransferase activator activity / negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / response to host immune response / positive regulation of catalytic activity / positive regulation of DNA binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / negative regulation of protein binding / manganese ion 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 / ATP binding / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.01 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 | 6b2p.cif.gz | 114.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b2p.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 6b2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/6b2p ftp://data.pdbj.org/pub/pdb/validation_reports/b2/6b2p | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30287.154 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pknB / Production host: Escherichia coli (E. coli) References: UniProt: P9WI80, UniProt: P9WI81*PLUS, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-CJJ / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 25% (w/v) PEGMME 2000, 0.1 M Tris-HCI pH 8.5, 400 mM magnesium chloride |
-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: Jun 22, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.011→58.976 Å / Num. obs: 6695 / % possible obs: 97.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 110.36 Å2 / Net I/σ(I): 15.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 3.01→58.98 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.837 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.417
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Displacement parameters | Biso mean: 112.79 Å2
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Refine analyze | Luzzati coordinate error obs: 0.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.01→58.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.01→3.37 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 92.9238 Å / Origin y: 78.2034 Å / Origin z: 19.2549 Å
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Refinement TLS group | Selection details: { A|* } |