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- PDB-5p9k: CRYSTAL STRUCTURE OF BTK with CNX 774 -

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Entry
Database: PDB / ID: 5p9k
TitleCRYSTAL STRUCTURE OF BTK with CNX 774
ComponentsTyrosine-protein kinase BTK
KeywordsTRANSFERASE / LEAD OPTIMIZATION
Function / homologySH2 domain / PH domain profile. / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / Pleckstrin homology domain / ER-Phagosome pathway / Zinc finger Btk-type profile. / Protein kinase domain profile. / SH3 domain / Zinc finger, Btk motif / Src homology 3 (SH3) domain profile. ...SH2 domain / PH domain profile. / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / Pleckstrin homology domain / ER-Phagosome pathway / Zinc finger Btk-type profile. / Protein kinase domain profile. / SH3 domain / Zinc finger, Btk motif / Src homology 3 (SH3) domain profile. / Protein kinase-like domain superfamily / Src homology 2 (SH2) domain profile. / SH3 domain / Tyrosine protein kinases specific active-site signature. / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinases ATP-binding region signature. / Protein tyrosine kinase / BTK motif / PH domain / Tyrosine-protein kinase, active site / Regulation of actin dynamics for phagocytic cup formation / Protein kinase domain / IRAK4 deficiency (TLR2/4) / SH2 domain superfamily / SH3-like domain superfamily / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Tyrosine-protein kinase BTK, SH3 domain / PH-like domain superfamily / RHO GTPases Activate WASPs and WAVEs / G beta:gamma signalling through BTK / Tyrosine-protein kinase, catalytic domain / MyD88 deficiency (TLR2/4) / G alpha (12/13) signalling events / G alpha (q) signalling events / FCERI mediated Ca+2 mobilization / DAP12 signaling / Protein kinase, ATP binding site / SH2 domain / regulation of B cell cytokine production / positive regulation of type III hypersensitivity / histamine secretion by mast cell / regulation of B cell apoptotic process / B cell affinity maturation / cellular response to molecule of fungal origin / negative regulation of cytokine production / positive regulation of B cell differentiation / cellular response to interleukin-7 / positive regulation of type I hypersensitivity / B cell activation / mesoderm development / negative regulation of B cell proliferation / phosphatidylinositol-3,4,5-trisphosphate binding / mast cell granule / cell maturation / calcium-mediated signaling / MyD88-dependent toll-like receptor signaling pathway / apoptotic signaling pathway / cellular response to reactive oxygen species / I-kappaB kinase/NF-kappaB signaling / non-specific protein-tyrosine kinase / peptidyl-tyrosine autophosphorylation / Fc-epsilon receptor signaling pathway / non-membrane spanning protein tyrosine kinase activity / peptidyl-tyrosine phosphorylation / B cell receptor signaling pathway / adaptive immune response / T cell receptor signaling pathway / cytoplasmic vesicle / positive regulation of NF-kappaB transcription factor activity / protein tyrosine kinase activity / intracellular signal transduction / membrane raft / innate immune response / protein phosphorylation / perinuclear region of cytoplasm / ATP binding / identical protein binding / plasma membrane / metal ion binding / nucleus / cytosol / cytoplasm / Tyrosine-protein kinase BTK
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / 1.28 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 20, 2016 / Release: May 24, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 24, 2017Structure modelrepositoryInitial release
1.1Feb 21, 2018Structure modelStructure summarypdbx_deposit_group_pdbx_deposit_group.group_type

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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)32,8282
Polyers32,3261
Non-polymers5021
Water6,864381
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)71.791, 104.107, 38.098
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP 21 21 2

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Components

#1: Protein/peptide 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: (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-7G8 / 4-[4-[[5-fluoranyl-4-[[3-(propanoylamino)phenyl]amino]pyrimidin-2-yl]amino]phenoxy]-~{N}-methyl-pyridine-2-carboxamide


Mass: 501.512 Da / Num. of mol.: 1 / Formula: C26H24FN7O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Formula: H2O / Water

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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 / Density percent sol: 44.14 %
Crystal growTemp: 298 K / Method: vapor diffusion / pH: 7 / Details: PEG 3350, sodium actate, BisTrisPropane

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98, 1.00
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Collection date: Mar 3, 2012
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength
IDWavelengthRelative weight
10.981.0
21.001.0
ReflectionD resolution high: 1.28 Å / D resolution low: 50.1 Å / Number obs: 73158 / Observed criterion sigma I: 0 / Rmerge I obs: 0.066 / NetI over sigmaI: 25.24 / Redundancy: 5.9 % / Percent possible obs: 97.7
Reflection shellRmerge I obs: 0.589 / Highest resolution: 1.28 Å / Lowest resolution: 1.33 Å / MeanI over sigI obs: 3.31 / Redundancy: 6 % / Percent possible all: 97.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationContact authorContact author emailDateLanguageLocationType
REFMAC5.2.0005refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extractionPDBdeposit[at]deposit.rcsb.orgJuly. 13, 2016C++http://sw-tools.pdb.org/apps/PDB_EXTRACT/package
HKL-2000data reduction
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1USJA

Correlation coeff Fo to Fc: 0.966 / Correlation coeff Fo to Fc free: 0.962
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Occupancy max: 1 / Occupancy min: 0.3 / Overall SU B: 1.494 / Overall SU ML: 0.03 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R: 0.051 / Overall ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.4 Å / Solvent model details: MASK
Displacement parametersB iso max: 61.6 Å2 / B iso mean: 19.5302 Å2 / B iso min: 8.22 Å2 / Aniso B11: 0.49 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -0.19 Å2 / Aniso B23: 0 Å2 / Aniso B33: -0.29 Å2
Least-squares processR factor R free: 0.1946 / R factor R work: 0.18 / Highest resolution: 1.28 Å / Lowest resolution: 59.1 Å / Number reflection R free: 3684 / Number reflection R work: 69419 / Number reflection obs: 73103 / Percent reflection R free: 5 / Percent reflection obs: 97.5
Refine hist #LASTHighest resolution: 1.28 Å / Lowest resolution: 59.1 Å
Number of atoms included #LASTProtein: 2214 / Nucleic acid: 0 / Ligand: 37 / Solvent: 381 / Total: 2632
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222444
X-RAY DIFFRACTIONr_bond_other_d0.0010.0202167
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9793317
X-RAY DIFFRACTIONr_angle_other_deg2.3033.0005065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0365.000302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.51224.018112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96215.000447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.21415.00014
X-RAY DIFFRACTIONr_chiral_restr0.0710.200342
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0202782
X-RAY DIFFRACTIONr_gen_planes_other0.0070.020534
Refine LS shellHighest resolution: 1.277 Å / R factor R free: 0.324 / R factor R work: 0.31 / Lowest resolution: 1.31 Å / Number reflection R free: 248 / Number reflection R work: 4820 / Number reflection all: 5068 / Total number of bins used: 20 / Percent reflection obs: 93.56
Refine TLSMethod: refined / L11: 0.0819 deg.2 / L12: 0.0364 deg.2 / L13: -0.0397 deg.2 / L22: 0.2423 deg.2 / L23: -0.0348 deg.2 / L33: 0.4184 deg.2 / S11: -0.0045 Å deg. / S12: -0.0066 Å deg. / S13: -0.0139 Å deg. / S21: -0.0143 Å deg. / S22: 0.0156 Å deg. / S23: -0.0176 Å deg. / S31: 0.0597 Å deg. / S32: 0.038 Å deg. / S33: -0.0111 Å deg. / T11: 0.0099 Å2 / T12: 0.0067 Å2 / T13: -0.0019 Å2 / T22: 0.0106 Å2 / T23: -0.0026 Å2 / T33: 0.0173 Å2 / Origin x: 16.1297 Å / Origin y: 16.1507 Å / Origin z: 5.845 Å

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