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- PDB-6tvn: Crystal Structure of 5-bromoindoline-2,3-dione covalently bound t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tvn | ||||||
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Title | Crystal Structure of 5-bromoindoline-2,3-dione covalently bound to the PH domain of Bruton's tyrosine kinase | ||||||
![]() | Tyrosine-protein kinase BTK | ||||||
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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) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of B cell differentiation / positive regulation of immunoglobulin production / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of interleukin-10 production / phospholipase activator activity / B cell activation / negative regulation of B cell proliferation / Fc-epsilon receptor signaling pathway / mesoderm development / phosphatidylinositol-3,4,5-trisphosphate binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brear, P. / Wagstaff, J. / Hyvonen, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of 1-methylindoline-2,3-dione covalently bound to the PH domain of Bruton's tyrosine kinase mutant R28C Authors: Brear, P. / Fischer, G. / May, M. / Pantelejevs, T. / Mathieu, R. / Rossmann, M. / Wagstaff, J. / Blaszczyk, B. / Hyvonen, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.7 KB | Display | ![]() |
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PDB format | ![]() | 111.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6tseC ![]() 6tt2C ![]() 6tuhC ![]() 1btkS 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19950.949 Da / Num. of mol.: 4 / Fragment: PH DOMAIN AND BTK MOTIF / Mutation: C145A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q06187, ![]() #2: Chemical | ChemComp-NYQ / #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.36 % / Mosaicity: 0 ° |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS 8.5 pH, 32.5% w/v PEG 3350, 200mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.31→66.45 Å / Num. obs: 30254 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 50.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.04 / Rrim(I) all: 0.104 / Net I/σ(I): 11.7 / Num. measured all: 201455 / Scaling rejects: 301 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1BTK Resolution: 2.31→66.45 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.393 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.362 / SU Rfree Blow DPI: 0.238 / SU Rfree Cruickshank DPI: 0.247
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Displacement parameters | Biso max: 136.23 Å2 / Biso mean: 53.75 Å2 / Biso min: 12.75 Å2
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Refinement step | Cycle: final / Resolution: 2.31→66.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.31→2.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
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