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- PDB-9ejs: Bruton's tyrosine kinase with mutations in the activation loop in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9ejs | ||||||
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Title | Bruton's tyrosine kinase with mutations in the activation loop in complex with compound PTI52 | ||||||
![]() | Tyrosine-protein kinase BTK | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / inhibitor / kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() G beta:gamma signalling through BTK / RHO GTPases Activate WASPs and WAVEs / G alpha (12/13) signalling events / FCERI mediated Ca+2 mobilization / G alpha (q) signalling events / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / monocyte proliferation / positive regulation of interleukin-17A production / Regulation of actin dynamics for phagocytic cup formation / eosinophil homeostasis ...G beta:gamma signalling through BTK / RHO GTPases Activate WASPs and WAVEs / G alpha (12/13) signalling events / FCERI mediated Ca+2 mobilization / G alpha (q) signalling events / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / monocyte proliferation / positive regulation of interleukin-17A production / Regulation of actin dynamics for phagocytic cup formation / eosinophil homeostasis / proteoglycan catabolic process / positive regulation of type III hypersensitivity / B cell affinity maturation / positive regulation of synoviocyte proliferation / histamine secretion by mast cell / neutrophil homeostasis / positive regulation of cGAS/STING signaling pathway / cellular response to molecule of fungal origin / positive regulation of type I hypersensitivity / cellular response to interleukin-7 / DAP12 signaling / negative regulation of cytokine production / positive regulation of immunoglobulin production / phospholipase activator activity / negative regulation of interleukin-10 production / negative regulation of B cell proliferation / positive regulation of NLRP3 inflammasome complex assembly / phosphatidylinositol-3,4,5-trisphosphate binding / phospholipase binding / cell maturation / positive regulation of B cell proliferation / positive regulation of phagocytosis / cellular response to reactive oxygen species / B cell receptor signaling pathway / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / cytoplasmic vesicle / protein tyrosine kinase activity / response to lipopolysaccharide / intracellular signal transduction / membrane raft / innate immune response / apoptotic process / perinuclear region of cytoplasm / zinc ion binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, D.Y. / Andreotti, A.H. / Tonge, P.J. / Bravo, E. / Li, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Modulating the Binding Kinetics of Bruton's Tyrosine Kinase Inhibitors through Transition-State Effects Authors: Bravo, E.J. / Li, Y. / Lin, D.Y.W. / Srinivasan, B. / Barone, M. / Li, S.X. / DelloRusso, F. / Rahiyanath, A.S. / Corrionero, A. / Alfonso, P. / Prendiville, N. / Kozakov, D. / Andreotti, A.H. / Tonge, P.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 582.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 39.5 KB | Display | |
Data in CIF | ![]() | 50.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9ejjC ![]() 9ejrC ![]() 9ejxC ![]() 9me2C ![]() 9me3C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Unit cell |
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Components
#1: Protein | Mass: 31821.521 Da / Num. of mol.: 3 / Mutation: K430R, L542M, S543T, V555T, R562K, S564A, P565S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P35991, non-specific protein-tyrosine kinase #2: Chemical | Mass: 522.601 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C29H30N8O2 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-DMS / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: Sodium citrate tribasic dihydrate pH 5.5, 16% w/v Polyethylene glycol 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 25, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.920153 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→34.16 Å / Num. obs: 32319 / % possible obs: 65.3 % / Redundancy: 5.2 % / Biso Wilson estimate: 28.93 Å2 / CC1/2: 0.976 / CC star: 0.994 / Net I/σ(I): 4.25 |
Reflection shell | Resolution: 2.26→2.35 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.653 / Mean I/σ(I) obs: 0.86 / Num. unique obs: 3542 / CC1/2: 0.33 / CC star: 0.705 / R split: 0.7809 / Rrim(I) all: 1.835 / % possible all: 2.49 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→19.99 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -54.5257340045 Å / Origin y: -8.76786422864 Å / Origin z: -31.4280768202 Å
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Refinement TLS group | Selection details: all |