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- PDB-5p9i: BTK1 SOAKED WITH IBRUTINIB-Rev -

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Basic information

Entry
Database: PDB / ID: 5p9i
TitleBTK1 SOAKED WITH IBRUTINIB-Rev
ComponentsTyrosine-protein kinase BTK
KeywordsTRANSFERASE / PROTEIN KINASE
Function / homology
Function and homology information


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 / histamine secretion by mast cell / positive regulation of synoviocyte proliferation ...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 / histamine secretion by mast cell / positive regulation of synoviocyte proliferation / 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 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 / phosphatidylinositol-3,4,5-trisphosphate binding / phospholipase binding / mesoderm development / positive regulation of immunoglobulin production / RHO GTPases Activate WASPs and WAVEs / positive regulation of phagocytosis / positive regulation of B cell proliferation / cell maturation / FCERI mediated Ca+2 mobilization / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / apoptotic signaling pathway / calcium-mediated signaling / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / G beta:gamma signalling through BTK / Regulation of actin dynamics for phagocytic cup formation / cellular response to reactive oxygen species / positive regulation of interleukin-6 production / peptidyl-tyrosine phosphorylation / G alpha (12/13) signalling events / positive regulation of tumor necrosis factor production / DAP12 signaling / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / T cell receptor signaling pathway / cytoplasmic vesicle / G alpha (q) signalling events / protein tyrosine kinase activity / Potential therapeutics for SARS / response to lipopolysaccharide / adaptive immune response / intracellular signal transduction / membrane raft / protein phosphorylation / innate immune response / perinuclear region of cytoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tyrosine-protein kinase BTK, SH3 domain / Zinc finger, Btk motif / BTK motif / Zinc finger Btk-type profile. / Bruton's tyrosine kinase Cys-rich motif / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain ...Tyrosine-protein kinase BTK, SH3 domain / Zinc finger, Btk motif / BTK motif / Zinc finger Btk-type profile. / Bruton's tyrosine kinase Cys-rich motif / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Src homology 3 domains / SH2 domain / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-1E8 / Tyrosine-protein kinase BTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / molecular replacement / Resolution: 1.11 Å
AuthorsGardberg, A.S.
CitationJournal: Mol. Pharmacol. / Year: 2017
Title: Ability of Bruton's Tyrosine Kinase Inhibitors to Sequester Y551 and Prevent Phosphorylation Determines Potency for Inhibition of Fc Receptor but not B-Cell Receptor Signaling.
Authors: Bender, A.T. / Gardberg, A. / Pereira, A. / Johnson, T. / Wu, Y. / Grenningloh, R. / Head, J. / Morandi, F. / Haselmayer, P. / Liu-Bujalski, L.
History
DepositionSep 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 1.2Nov 17, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / pdbx_deposit_group
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase BTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9234
Polymers32,3261
Non-polymers5973
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.611, 104.579, 38.021
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Tyrosine-protein kinase BTK / Agammaglobulinemia tyrosine kinase / ATK / B-cell progenitor kinase / BPK / Bruton tyrosine kinase


Mass: 32326.068 Da / Num. of mol.: 1 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTK, AGMX1, ATK, BPK / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5
References: UniProt: Q06187, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-1E8 / 1-{(3R)-3-[4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl}prop-2-en-1-one / Imbruvica / PCI-32765 / Ibrutinib


Mass: 440.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H24N6O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: PEG 3350, sodium actate, BisTrisPropane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.11→50 Å / Num. obs: 112485 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 6.22 % / Biso Wilson estimate: 10.66 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.54
Reflection shellResolution: 1.11→1.18 Å / Redundancy: 5.71 % / Rmerge(I) obs: 1.81 / Mean I/σ(I) obs: 0.91 / Rejects: 0 / % possible all: 93.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.11→42.23 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9326 / SU R Cruickshank DPI: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.034 / SU Rfree Blow DPI: 0.035 / SU Rfree Cruickshank DPI: 0.034
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 5615 5 %RANDOM
Rwork0.1957 ---
obs0.1964 112300 98.93 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 87.26 Å2 / Biso mean: 17.81 Å2 / Biso min: 7.42 Å2
Baniso -1Baniso -2Baniso -3
1--2.9892 Å20 Å20 Å2
2--1.4304 Å20 Å2
3---1.5588 Å2
Refine analyzeLuzzati coordinate error obs: 0.141 Å
Refinement stepCycle: final / Resolution: 1.11→42.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 41 182 2372
Biso mean--16.1 23.03 -
Num. residues----271
LS refinement shellResolution: 1.11→1.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2445 389 4.99 %
Rwork0.2537 7404 -
all0.2532 7793 -
obs--98.93 %
Refinement TLS params.Method: refined / Origin x: -19.7489 Å / Origin y: 16.2373 Å / Origin z: -13.0892 Å
111213212223313233
T-0.0161 Å20.0035 Å2-0.0023 Å2--0.0138 Å2-0.0001 Å2---0.028 Å2
L0.1885 °20.0541 °2-0.0689 °2-0.4335 °20.0293 °2--0.4183 °2
S0.0017 Å °-0.0213 Å °-0.0207 Å °0.0231 Å °0.0065 Å °-0.0059 Å °0.0661 Å °0.0244 Å °-0.0081 Å °
Refinement TLS groupSelection details: { A|* }

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