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Open data
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Basic information
Entry | Database: PDB / ID: 7kxm | ||||||
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Title | BTK1 SOAKED WITH COMPOUND 5, Y551 IS SEQUESTERED | ||||||
![]() | Tyrosine-protein kinase BTK | ||||||
![]() | TRANSFERASE / PROTEIN KINASE | ||||||
Function / homology | ![]() regulation of B cell cytokine production / proteoglycan catabolic process / monocyte proliferation / positive regulation of interleukin-17A production / regulation of B cell apoptotic process / eosinophil homeostasis / positive regulation of type III hypersensitivity / B cell affinity maturation / positive regulation of synoviocyte proliferation / histamine secretion by mast cell ...regulation of B cell cytokine production / proteoglycan catabolic process / monocyte proliferation / positive regulation of interleukin-17A production / regulation of B cell apoptotic process / eosinophil homeostasis / positive regulation of type III hypersensitivity / B cell affinity maturation / positive regulation of synoviocyte proliferation / histamine secretion by mast cell / neutrophil homeostasis / cellular response to molecule of fungal origin / positive regulation of type I hypersensitivity / cellular response to interleukin-7 / MyD88 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / IRAK4 deficiency (TLR2/4) / positive regulation of immunoglobulin production / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of B cell differentiation / positive regulation of NLRP3 inflammasome complex assembly / phospholipase activator activity / negative regulation of interleukin-10 production / B cell activation / negative regulation of B cell proliferation / Fc-epsilon receptor signaling pathway / mesoderm development / phosphatidylinositol-3,4,5-trisphosphate binding / phospholipase binding / RHO GTPases Activate WASPs and WAVEs / positive regulation of B cell proliferation / positive regulation of phagocytosis / cell maturation / FCERI mediated Ca+2 mobilization / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calcium-mediated signaling / apoptotic signaling pathway / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Regulation of actin dynamics for phagocytic cup formation / G beta:gamma signalling through BTK / cellular response to reactive oxygen species / peptidyl-tyrosine phosphorylation / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / G alpha (12/13) signalling events / DAP12 signaling / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / ER-Phagosome pathway / cytoplasmic vesicle / G alpha (q) signalling events / protein tyrosine kinase activity / adaptive immune response / Potential therapeutics for SARS / response to lipopolysaccharide / intracellular signal transduction / membrane raft / protein phosphorylation / innate immune response / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gardberg, A. | ||||||
![]() | ![]() Title: Discovery of potent and selective reversible Bruton's tyrosine kinase inhibitors. Authors: Qiu, H. / Ali, Z. / Bender, A. / Caldwell, R. / Chen, Y.Y. / Fang, Z. / Gardberg, A. / Glaser, N. / Goettsche, A. / Goutopoulos, A. / Grenningloh, R. / Hanschke, B. / Head, J. / Johnson, T. ...Authors: Qiu, H. / Ali, Z. / Bender, A. / Caldwell, R. / Chen, Y.Y. / Fang, Z. / Gardberg, A. / Glaser, N. / Goettsche, A. / Goutopoulos, A. / Grenningloh, R. / Hanschke, B. / Head, J. / Johnson, T. / Jones, C. / Jones, R. / Kulkarni, S. / Maurer, C. / Morandi, F. / Neagu, C. / Poetzsch, S. / Potnick, J. / Schmidt, R. / Roe, K. / Viacava Follis, A. / Wing, C. / Zhu, X. / Sherer, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.4 KB | Display | ![]() |
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PDB format | ![]() | 98.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 675.5 KB | Display | ![]() |
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Full document | ![]() | 676.5 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kxlC ![]() 7kxnC ![]() 7kxoC ![]() 7kxpC ![]() 7kxqC ![]() 1k2pS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 31598.287 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q06187, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-X9M / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 3350 0.1 M Bis Tris Propane pH 7.5 0.2 M Sodium acetate trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→50 Å / Num. obs: 67021 / % possible obs: 99.3 % / Redundancy: 5.82 % / Biso Wilson estimate: 19.25 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.62 |
Reflection shell | Resolution: 1.33→1.41 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.45 / Mean I/σ(I) obs: 0.87 / Num. unique obs: 67021 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1k2p Resolution: 1.33→42.29 Å / Cor.coef. Fo:Fc: 0.9524 / Cor.coef. Fo:Fc free: 0.819 / SU R Cruickshank DPI: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.057 / SU Rfree Blow DPI: 0.064 / SU Rfree Cruickshank DPI: 0.063
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Displacement parameters | Biso max: 116.31 Å2 / Biso mean: 24.45 Å2 / Biso min: 10.14 Å2
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Refine analyze | Luzzati coordinate error obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.33→42.29 Å
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LS refinement shell | Resolution: 1.33→1.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 16.1393 Å / Origin y: 16.3014 Å / Origin z: 6.033 Å
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Refinement TLS group | Selection details: { A|* } |