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- PDB-6aub: CRYSTAL STRUCTURE OF BRUTON'S TYROSINE KINASE IN COMPLEX WITH INH... -

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Basic information

Entry
Database: PDB / ID: 6aub
TitleCRYSTAL STRUCTURE OF BRUTON'S TYROSINE KINASE IN COMPLEX WITH INHIBITOR CGI2815
ComponentsTyrosine-protein kinase BTK
KeywordsTransferase/Transferase Inhibitor / BTK / Transferase-Transferase Inhibitor complex
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 / nucleus / metal ion binding / cytosol / cytoplasm / Tyrosine-protein kinase BTK
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.65 Å resolution
AuthorsDavies, D.R. / Staker, B.L.
CitationJournal: TO BE PUBLISHED
Title: To Be Determined
Authors: Ortwine, D.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 31, 2017 / Release: Sep 12, 2018

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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)31,7334
Polyers30,9621
Non-polymers7723
Water3,279182
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)108.489, 108.489, 42.078
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP 61

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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: 30961.631 Da / Num. of mol.: 1 / Fragment: UNP residues 429-691 / Source: (gene. exp.) Homo sapiens (human) / Gene: BTK, AGMX1, ATK, BPK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q06187, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Formula: SO4 / Sulfate
#3: Chemical ChemComp-BXM / 4-tert-butyl-N-[2-methyl-3-(1-methyl-5-{[5-(morpholine-4-carbonyl)pyridin-2-yl]amino}-6-oxo-1,6-dihydropyridin-3-yl)phenyl]benzamide


Mass: 579.689 Da / Num. of mol.: 1 / Formula: C34H37N5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.31 / Density percent sol: 46.73 %
Crystal growTemp: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 MM IMIDAZOLE PH 7.0, 14% PEG 10,000, 200 MM LI2SO4, 10 MM BETA MERCAPTOETHANOL, 0.75% (W/V) s-BOG

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 19-BM / Synchrotron site: APS / Beamline: 19-BM / Wavelength: 1
DetectorType: RIGAKU / Detector: CCD / Collection date: Jun 1, 2006
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionD resolution high: 1.65 Å / D resolution low: 5 Å / Number obs: 34147 / Rsym value: 0.075 / NetI over sigmaI: 18.3 / Redundancy: 5 % / Percent possible obs: 99.8
Reflection shellHighest resolution: 1.65 Å / Lowest resolution: 1.7 Å / MeanI over sigI obs: 2.6 / Number unique obs: 2383 / Rsym value: 0.434 / Redundancy: 4.9 % / Percent possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXDEV_2863refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OCS
Overall SU ML: 0.17 / Cross valid method: FREE R-VALUE / Sigma F: 1.34 / Overall phase error: 18.51
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Displacement parametersB iso max: 59.37 Å2 / B iso mean: 21.1996 Å2 / B iso min: 8.61 Å2
Least-squares processR factor R free: 0.199 / R factor R work: 0.166 / Highest resolution: 1.65 Å / Lowest resolution: 27.14 Å / Number reflection R free: 1726 / Number reflection obs: 34147 / Percent reflection R free: 5.05 / Percent reflection obs: 99.7
Refine hist #finalHighest resolution: 1.65 Å / Lowest resolution: 27.14 Å / B iso mean ligand: 21.53 / B iso mean solvent: 30.83 / Number residues total: 264
Number of atoms included #finalProtein: 2105 / Nucleic acid: 0 / Ligand: 53 / Solvent: 182 / Total: 2340
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 12

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
1.65000.26900.22151.70001162673278999.0000
1.65110.26900.22151.69971162673278999.0000
1.69970.23380.19961.754614026972837100.0000
1.75460.24190.19381.817313326782811100.0000
1.81730.19270.17731.890014526902835100.0000
1.89000.18950.16571.976015226902842100.0000
1.97600.21440.15742.080214727032850100.0000
2.08020.18110.15462.210415526922847100.0000
2.21040.20270.15552.381013426792813100.0000
2.38100.20830.16662.620414127142855100.0000
2.62040.20260.17912.999216427072871100.0000
2.99920.19120.15933.777116127232884100.0000

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