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- PDB-4yjt: THE KINASE DOMAIN OF HUMAN SPLEEN TYROSINE (SYK) IN COMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 4yjt
TitleTHE KINASE DOMAIN OF HUMAN SPLEEN TYROSINE (SYK) IN COMPLEX WITH GTC000233
ComponentsTyrosine-protein kinase SYK
KeywordsTRANSFERASE / SYK / NON-RECEPTOR TYROSINE KINASE / SPLEEN TYROSINE KINASE / PHOSPHORYLATION / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Function / homology
Function and homology information


interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonic acid secretion / cellular response to lectin / serotonin secretion by platelet / positive regulation of interleukin-3 production / gamma-delta T cell differentiation / positive regulation of gamma-delta T cell differentiation / B cell receptor complex ...interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonic acid secretion / cellular response to lectin / serotonin secretion by platelet / positive regulation of interleukin-3 production / gamma-delta T cell differentiation / positive regulation of gamma-delta T cell differentiation / B cell receptor complex / Toll-like receptor binding / regulation of platelet aggregation / positive regulation of alpha-beta T cell proliferation / neutrophil activation involved in immune response / leukocyte activation involved in immune response / positive regulation of mast cell cytokine production / regulation of platelet activation / lymph vessel development / collagen-activated tyrosine kinase receptor signaling pathway / cell activation / positive regulation of mast cell degranulation / positive regulation of killing of cells of another organism / regulation of phagocytosis / beta selection / macrophage activation involved in immune response / early phagosome / cellular response to molecule of fungal origin / leukotriene biosynthetic process / FLT3 signaling through SRC family kinases / regulation of tumor necrosis factor-mediated signaling pathway / cellular response to lipid / positive regulation of monocyte chemotactic protein-1 production / interleukin-3-mediated signaling pathway / regulation of DNA-binding transcription factor activity / positive regulation of cell adhesion mediated by integrin / positive regulation of granulocyte macrophage colony-stimulating factor production / Fc epsilon receptor (FCERI) signaling / Interleukin-2 signaling / blood vessel morphogenesis / positive regulation of alpha-beta T cell differentiation / T cell receptor complex / positive regulation of B cell differentiation / leukocyte cell-cell adhesion / mast cell degranulation / Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of interleukin-4 production / Dectin-2 family / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / phospholipase binding / positive regulation of interleukin-10 production / positive regulation of receptor internalization / cellular response to low-density lipoprotein particle stimulus / FCGR activation / positive regulation of type I interferon production / phosphatase binding / positive regulation of bone resorption / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / positive regulation of calcium-mediated signaling / Signaling by CSF3 (G-CSF) / negative regulation of inflammatory response to antigenic stimulus / GPVI-mediated activation cascade / positive regulation of TORC1 signaling / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of interleukin-12 production / phosphotyrosine residue binding / Integrin signaling / SH2 domain binding / FCERI mediated Ca+2 mobilization / B cell differentiation / FCGR3A-mediated IL10 synthesis / neutrophil chemotaxis / regulation of ERK1 and ERK2 cascade / positive regulation of superoxide anion generation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of interleukin-8 production / integrin-mediated signaling pathway / Regulation of signaling by CBL / calcium-mediated signaling / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / animal organ morphogenesis / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / positive regulation of protein-containing complex assembly / Inactivation of CSF3 (G-CSF) signaling / receptor internalization / platelet activation / Regulation of actin dynamics for phagocytic cup formation / CLEC7A (Dectin-1) signaling / peptidyl-tyrosine phosphorylation / protein import into nucleus / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / integrin binding / DAP12 signaling
Similarity search - Function
Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain ...Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / 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-4DQ / Tyrosine-protein kinase SYK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.52 Å
AuthorsSomers, D.O. / Neu, M. / Stuckey, J.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2011
Title: Discovery of GSK143, a highly potent, selective and orally efficacious spleen tyrosine kinase inhibitor.
Authors: Liddle, J. / Atkinson, F.L. / Barker, M.D. / Carter, P.S. / Curtis, N.R. / Davis, R.P. / Douault, C. / Dickson, M.C. / Elwes, D. / Garton, N.S. / Gray, M. / Hayhow, T.G. / Hobbs, C.I. / ...Authors: Liddle, J. / Atkinson, F.L. / Barker, M.D. / Carter, P.S. / Curtis, N.R. / Davis, R.P. / Douault, C. / Dickson, M.C. / Elwes, D. / Garton, N.S. / Gray, M. / Hayhow, T.G. / Hobbs, C.I. / Jones, E. / Leach, S. / Leavens, K. / Lewis, H.D. / McCleary, S. / Neu, M. / Patel, V.K. / Preston, A.G. / Ramirez-Molina, C. / Shipley, T.J. / Skone, P.A. / Smithers, N. / Somers, D.O. / Walker, A.L. / Watson, R.J. / Weingarten, G.G.
History
DepositionMar 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase SYK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3423
Polymers32,8111
Non-polymers5322
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-0 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.328, 87.214, 40.230
Angle α, β, γ (deg.)90.000, 92.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosine-protein kinase SYK / Spleen tyrosine kinase / p72-Syk


Mass: 32810.605 Da / Num. of mol.: 1 / Fragment: UNP residues 355-635
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYK / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P43405, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-4DQ / N~2~-(1,1-dioxido-2,3-dihydro-1,2-benzothiazol-6-yl)-N~4~-ethyl-5-fluoro-N~4~-(1H-indazol-4-yl)pyrimidine-2,4-diamine


Mass: 439.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18FN7O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% Jeffamine ED-2001, 10% Glycerol, 0.1M MES pH6.0, 5mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.44→27.535 Å / Num. obs: 48894 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.74 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/av σ(I): 6.82 / Net I/σ(I): 13.4 / Num. measured all: 180152
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym valueNet I/σ(I) obs% possible all
1.44-1.523.70.5011.32618871460.5012.3100
1.52-1.613.70.3221.22475367370.3223.7100
1.61-1.723.70.1973.72342763420.1976.2100
1.72-1.863.70.1275.62183258960.1279.5100
1.86-2.043.70.0863.62019554410.08614.4100
2.04-2.283.70.0594.21827249140.05919.2100
2.28-2.633.70.04813.51621743590.04822.9100
2.63-3.223.70.04711.61365536840.04727.499.9
3.22-4.553.70.036171040428470.03633.499.8
4.55-29.5533.40.03616.5520915280.03632.196.2

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Processing

Software
NameVersionClassification
MOSFLM6.2.4data reduction
SCALA3.2.5data scaling
BUSTER2.11.2refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: In-house SYK model

Resolution: 1.52→27.53 Å / Cor.coef. Fo:Fc: 0.9623 / Cor.coef. Fo:Fc free: 0.9517 / SU R Cruickshank DPI: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.079 / SU Rfree Blow DPI: 0.081 / SU Rfree Cruickshank DPI: 0.079
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 2075 4.99 %RANDOM
Rwork0.1743 ---
obs0.176 41545 99.82 %-
Displacement parametersBiso max: 105.97 Å2 / Biso mean: 24.51 Å2 / Biso min: 9.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.7175 Å20 Å2-0.4624 Å2
2--0.7151 Å20 Å2
3---1.0025 Å2
Refine analyzeLuzzati coordinate error obs: 0.169 Å
Refinement stepCycle: final / Resolution: 1.52→27.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 37 315 2550
Biso mean--22.83 34.76 -
Num. residues----270
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1087SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes337HARMONIC5
X-RAY DIFFRACTIONt_it2357HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion271SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3022SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2357HARMONIC20.011
X-RAY DIFFRACTIONt_angle_deg3207HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion3.95
X-RAY DIFFRACTIONt_other_torsion2.66
LS refinement shellResolution: 1.52→1.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2371 146 4.79 %
Rwork0.21 2901 -
all0.2113 3047 -
obs--99.82 %
Refinement TLS params.Method: refined / Origin x: 33.383 Å / Origin y: 27.7204 Å / Origin z: 36.2076 Å
111213212223313233
T-0.0288 Å2-0.0106 Å20.0065 Å2--0.0315 Å2-0.024 Å2---0.0387 Å2
L0.5263 °2-0.4008 °20.1186 °2-0.815 °2-0.1213 °2--0.6582 °2
S-0.0024 Å °0.0313 Å °-0.0328 Å °0.0221 Å °-0.0318 Å °-0.0576 Å °-0.038 Å °0.0179 Å °0.0342 Å °
Refinement TLS groupSelection details: {A|*}

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