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- PDB-8xq2: Crystal structure of spleen tyrosine kinase(SYK)in complex with S... -

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Basic information

Entry
Database: PDB / ID: 8xq2
TitleCrystal structure of spleen tyrosine kinase(SYK)in complex with SKI-G-1693
ComponentsTyrosine-protein kinase SYK
KeywordsSIGNALING PROTEIN-INHIBITOR / SIGNALING PROTEIN-Inhibitor complex
Function / homology
Function and homology information


interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / positive regulation of interleukin-3 production / gamma-delta T cell differentiation / positive regulation of gamma-delta T cell differentiation / cellular response to lectin / B cell receptor complex / regulation of platelet aggregation ...interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / positive regulation of interleukin-3 production / gamma-delta T cell differentiation / positive regulation of gamma-delta T cell differentiation / cellular response to lectin / B cell receptor complex / regulation of platelet aggregation / Toll-like receptor binding / serotonin secretion by platelet / positive regulation of alpha-beta T cell proliferation / leukocyte activation involved in immune response / positive regulation of mast cell cytokine production / neutrophil activation involved in immune response / cell surface pattern recognition receptor signaling pathway / positive regulation of mast cell degranulation / lymph vessel development / collagen-activated tyrosine kinase receptor signaling pathway / regulation of platelet activation / cell activation / beta selection / cellular response to molecule of fungal origin / FLT3 signaling through SRC family kinases / early phagosome / leukotriene biosynthetic process / regulation of phagocytosis / macrophage activation involved in immune response / regulation of tumor necrosis factor-mediated signaling pathway / interleukin-3-mediated signaling pathway / positive regulation of monocyte chemotactic protein-1 production / cellular response to lipid / regulation of DNA-binding transcription factor activity / Fc epsilon receptor (FCERI) signaling / Interleukin-2 signaling / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of cell adhesion mediated by integrin / positive regulation of alpha-beta T cell differentiation / blood vessel morphogenesis / positive regulation of B cell differentiation / leukocyte cell-cell adhesion / T cell receptor complex / mast cell degranulation / Dectin-2 family / positive regulation of interleukin-4 production / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / phospholipase binding / amyloid-beta clearance / positive regulation of interleukin-10 production / positive regulation of receptor internalization / cellular response to low-density lipoprotein particle stimulus / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / positive regulation of type I interferon production / Role of phospholipids in phagocytosis / positive regulation of bone resorption / phosphatase binding / regulation of ERK1 and ERK2 cascade / Signaling by CSF3 (G-CSF) / GPVI-mediated activation cascade / neutrophil chemotaxis / phosphotyrosine residue binding / positive regulation of interleukin-12 production / positive regulation of TORC1 signaling / Integrin signaling / FCERI mediated Ca+2 mobilization / B cell differentiation / SH2 domain binding / FCGR3A-mediated IL10 synthesis / positive regulation of calcium-mediated signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of superoxide anion generation / animal organ morphogenesis / integrin-mediated signaling pathway / positive regulation of interleukin-8 production / non-membrane spanning protein tyrosine kinase activity / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / positive regulation of protein-containing complex assembly / apoptotic signaling pathway / negative regulation of inflammatory response to antigenic stimulus / calcium-mediated signaling / Inactivation of CSF3 (G-CSF) signaling / peptidyl-tyrosine phosphorylation / receptor internalization / Regulation of actin dynamics for phagocytic cup formation / platelet activation / positive regulation of interleukin-6 production / CLEC7A (Dectin-1) signaling / cellular response to amyloid-beta / protein import into nucleus / positive regulation of tumor necrosis factor production / kinase activity / integrin binding
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-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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Tyrosine-protein kinase SYK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBong, S.M. / Lee, B.I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of spleen tyrosine kinase(SYK) in complex with SKI-G-1673
Authors: Lee, B.I.
History
DepositionJan 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase SYK
B: Tyrosine-protein kinase SYK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9615
Polymers67,8022
Non-polymers1,1593
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.949, 41.183, 87.351
Angle α, β, γ (deg.)98.961, 90.989, 100.694
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 33900.965 Da / Num. of mol.: 2 / Fragment: PROTEIN KINASE DOMAIN, RESIDUES 356-635
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYK / 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-A1LV7 / cyclopropyl-[1-(2-fluoranylethyl)-5-[[4-[4-[[(3~{R},4~{S})-3-methoxy-4-oxidanyl-pyrrolidin-1-yl]methyl]-3-methyl-pyrazol-1-yl]pyrimidin-2-yl]amino]indol-3-yl]methanone


Mass: 533.597 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H32FN7O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.06 Å3/Da / Density % sol: 40.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M tris-HCl pH 8.5, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 48626 / % possible obs: 96.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.35 Å2 / CC1/2: 0.913 / Net I/σ(I): 2.67
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 4695 / CC1/2: 0.913

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→39.93 Å / SU ML: 0.2112 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 24.3665
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2379 2461 5.08 %
Rwork0.2041 45938 -
obs0.2058 48399 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.26 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4270 0 84 142 4496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514456
X-RAY DIFFRACTIONf_angle_d0.7426005
X-RAY DIFFRACTIONf_chiral_restr0.0479625
X-RAY DIFFRACTIONf_plane_restr0.0059745
X-RAY DIFFRACTIONf_dihedral_angle_d13.91651672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.28071290.24342465X-RAY DIFFRACTION93.58
1.83-1.870.28731350.23022507X-RAY DIFFRACTION95.28
1.87-1.910.26741510.23352506X-RAY DIFFRACTION96.23
1.91-1.960.2781380.23422555X-RAY DIFFRACTION96.52
1.96-2.010.28551200.22692555X-RAY DIFFRACTION95.91
2.01-2.060.25131450.22032545X-RAY DIFFRACTION96.83
2.06-2.120.26531300.22062522X-RAY DIFFRACTION96.44
2.12-2.190.23791250.21622563X-RAY DIFFRACTION96.34
2.19-2.270.27581450.21972553X-RAY DIFFRACTION97.02
2.27-2.360.27731490.22162545X-RAY DIFFRACTION96.46
2.36-2.470.26411470.21672529X-RAY DIFFRACTION96.82
2.47-2.60.27721340.22042597X-RAY DIFFRACTION97.75
2.6-2.760.24361420.2292556X-RAY DIFFRACTION97.44
2.76-2.970.24661390.2232580X-RAY DIFFRACTION97.84
2.97-3.270.28821350.22392601X-RAY DIFFRACTION98.06
3.27-3.740.21931380.2052587X-RAY DIFFRACTION98.13
3.74-4.710.19181210.16592594X-RAY DIFFRACTION98.09
4.72-39.930.19511380.17362578X-RAY DIFFRACTION97.31

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