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- PDB-6bik: BTK complex with compound 7 -

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Basic information

Entry
Database: PDB / ID: 6bik
TitleBTK complex with compound 7
ComponentsTyrosine-protein kinase BTK
KeywordsSIGNALING PROTEIN / BTK / inhibitor / water structure / 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 / 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 / MyD88 deficiency (TLR2/4) / cellular response to interleukin-7 / MyD88-dependent toll-like receptor signaling pathway / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of immunoglobulin production / positive regulation of B cell differentiation / positive regulation of NLRP3 inflammasome complex assembly / phospholipase activator activity / negative regulation of interleukin-10 production / negative regulation of B cell proliferation / mesoderm development / Fc-epsilon receptor signaling pathway / B cell activation / phosphatidylinositol-3,4,5-trisphosphate binding / phospholipase binding / 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 / non-specific protein-tyrosine kinase / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / non-membrane spanning protein tyrosine kinase activity / calcium-mediated signaling / Regulation of actin dynamics for phagocytic cup formation / peptidyl-tyrosine phosphorylation / G beta:gamma signalling through BTK / positive regulation of interleukin-6 production / cellular response to reactive oxygen species / positive regulation of tumor necrosis factor production / G alpha (12/13) signalling events / DAP12 signaling / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / ER-Phagosome pathway / cytoplasmic vesicle / protein tyrosine kinase activity / G alpha (q) signalling events / adaptive immune response / response to lipopolysaccharide / Potential therapeutics for SARS / intracellular signal transduction / protein phosphorylation / membrane raft / innate immune response / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / 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 ...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 / SH2 domain / Src homology 3 domains / 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. / Tyrosine-protein kinase, active site / PH-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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-DTJ / Tyrosine-protein kinase BTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.901 Å
AuthorsKiefer, J.R. / Eigenbrot, C. / Yu, C.L.
CitationJournal: J. Comput. Aided Mol. Des. / Year: 2019
Title: Water molecules in protein-ligand interfaces. Evaluation of software tools and SAR comparison.
Authors: Nittinger, E. / Gibbons, P. / Eigenbrot, C. / Davies, D.R. / Maurer, B. / Yu, C.L. / Kiefer, J.R. / Kuglstatter, A. / Murray, J. / Ortwine, D.F. / Tang, Y. / Tsui, V.
History
DepositionNov 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase BTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8566
Polymers33,8791
Non-polymers9775
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.016, 108.016, 41.631
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 33878.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DTJ / 4-tert-butyl-N-[2-(hydroxymethyl)-3-(1-methyl-5-{[5-(morpholine-4-carbonyl)pyridin-2-yl]amino}-6-oxo-1,6-dihydropyridazin-3-yl)phenyl]benzamide


Mass: 596.676 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H36N6O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7 / Details: PEG 10000, Li2SO4, pH 7.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 20603 / % possible obs: 93.1 % / Redundancy: 4 % / Biso Wilson estimate: 23.02 Å2 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.053 / Rrim(I) all: 0.113 / Χ2: 1.01 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.932.10.4956610.5380.370.6230.7161.2
1.93-1.972.20.4277630.6470.3140.5340.68768.8
1.97-2.012.50.4288770.6570.2980.5260.75581.1
2.01-2.052.60.4169550.6930.2920.5120.74187.3
2.05-2.0930.35910320.7930.2360.4330.77792.3
2.09-2.143.20.33810720.8580.2110.40.85897.8
2.14-2.193.60.3410280.8510.2040.3990.83494.2
2.19-2.253.90.32110910.880.1820.3710.91499.5
2.25-2.324.20.31210540.8940.170.3570.93595.6
2.32-2.394.40.29410830.920.1580.3350.95199.6
2.39-2.484.50.26210640.9360.1360.2961.00796.4
2.48-2.584.60.23111070.9560.1190.2611.00498.7
2.58-2.74.70.19810680.9730.1010.2231.07998.5
2.7-2.844.70.16610950.980.0840.1861.11398.1
2.84-3.024.70.1310840.9860.0660.1461.14798.5
3.02-3.254.80.09211080.9930.0460.1041.09398.8
3.25-3.584.80.06810840.9960.0340.0761.10799.1
3.58-4.094.90.05211160.9980.0260.0591.10299.3
4.09-5.154.90.04810990.9980.0240.0531.22997.2
5.15-404.70.04111620.9980.0210.0461.02498.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
ADSCdata collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→35.357 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 1058 5.14 %
Rwork0.1609 --
obs0.1639 20598 93.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.901→35.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 65 171 2374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062293
X-RAY DIFFRACTIONf_angle_d0.8633108
X-RAY DIFFRACTIONf_dihedral_angle_d18.9141347
X-RAY DIFFRACTIONf_chiral_restr0.047322
X-RAY DIFFRACTIONf_plane_restr0.004395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9005-1.9870.258850.24241759X-RAY DIFFRACTION67
1.987-2.09180.28861520.20422292X-RAY DIFFRACTION89
2.0918-2.22280.24381430.18792499X-RAY DIFFRACTION97
2.2228-2.39440.22981410.18012545X-RAY DIFFRACTION98
2.3944-2.63530.22361500.1652550X-RAY DIFFRACTION98
2.6353-3.01650.22721540.16222562X-RAY DIFFRACTION99
3.0165-3.79970.22721140.14182642X-RAY DIFFRACTION99
3.7997-35.36260.17891190.14232691X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.466-0.39530.19841.1359-0.02551.08430.1139-0.1453-0.36780.2295-0.11180.10820.0537-0.0567-0.00730.2177-0.0528-0.00590.19730.00860.242993.6619-51.8118-7.0102
22.0190.740.29030.54970.82652.3057-0.14590.058-0.09390.0192-0.22670.65610.0936-0.46910.23910.2046-0.00530.05620.2708-0.04090.279994.5471-39.08912.277
31.73750.8578-0.75421.4867-0.40671.3921-0.06240.1477-0.16510.01520.05820.01510.1817-0.2151-0.02770.1802-0.0221-0.02070.2244-0.03350.215594.859-48.3234-5.8091
41.54460.1578-0.93511.4783-0.05051.92740.07110.11930.035-0.1491-0.0337-0.0354-0.1797-0.0765-0.03160.15840.0052-0.0210.17380.010.1428108.4852-30.9262-5.7009
51.3091-0.03350.39390.603-0.23980.98950.0537-0.1217-0.16040.1322-0.009-0.0320.0352-0.0557-0.04540.1664-0.0175-0.01860.1490.00620.1506110.6211-42.76953.4405
62.3856-1.20070.43053.1553-0.6051.2574-0.0340.1432-0.09340.114-0.0746-0.1790.16570.38910.09690.1683-0.023-0.01910.2182-0.01780.194125.6069-42.69690.3316
71.46350.1733-0.4581.34930.16681.8075-0.0808-0.04820.09490.1129-0.0125-0.144-0.17230.11290.10010.1952-0.0423-0.04850.1746-0.01160.1639117.3288-27.32565.1464
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 395 through 444 )
2X-RAY DIFFRACTION2chain 'A' and (resid 445 through 459 )
3X-RAY DIFFRACTION3chain 'A' and (resid 460 through 482 )
4X-RAY DIFFRACTION4chain 'A' and (resid 483 through 515 )
5X-RAY DIFFRACTION5chain 'A' and (resid 516 through 591 )
6X-RAY DIFFRACTION6chain 'A' and (resid 592 through 611 )
7X-RAY DIFFRACTION7chain 'A' and (resid 612 through 658 )

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