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- PDB-8haq: The complex of Src with GW8510 -

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Basic information

Entry
Database: PDB / ID: 8haq
TitleThe complex of Src with GW8510
ComponentsIsoform 2 of Proto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE / Src-GW8510 complex
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / positive regulation of dephosphorylation / regulation of toll-like receptor 3 signaling pathway / cellular response to progesterone stimulus / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / negative regulation of telomere maintenance / Regulation of gap junction activity / ERBB2 signaling pathway / positive regulation of integrin activation ...regulation of caveolin-mediated endocytosis / positive regulation of dephosphorylation / regulation of toll-like receptor 3 signaling pathway / cellular response to progesterone stimulus / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / negative regulation of telomere maintenance / Regulation of gap junction activity / ERBB2 signaling pathway / positive regulation of integrin activation / BMP receptor binding / negative regulation of focal adhesion assembly / Activated NTRK2 signals through FYN / intestinal epithelial cell development / focal adhesion assembly / Netrin mediated repulsion signals / negative regulation of neutrophil activation / bone resorption / positive regulation of small GTPase mediated signal transduction / connexin binding / Activated NTRK3 signals through PI3K / signal complex assembly / regulation of vascular permeability / Co-stimulation by CD28 / EPH-Ephrin signaling / podosome / positive regulation of lamellipodium morphogenesis / DCC mediated attractive signaling / regulation of bone resorption / Regulation of RUNX1 Expression and Activity / stress fiber assembly / Ephrin signaling / Signal regulatory protein family interactions / negative regulation of mitochondrial depolarization / leukocyte migration / MET activates PTK2 signaling / Regulation of KIT signaling / cellular response to peptide hormone stimulus / regulation of early endosome to late endosome transport / Signaling by ALK / phospholipase activator activity / GP1b-IX-V activation signalling / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / p130Cas linkage to MAPK signaling for integrins / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / positive regulation of Rac protein signal transduction / stimulatory C-type lectin receptor signaling pathway / Receptor Mediated Mitophagy / Signaling by EGFR / negative regulation of intrinsic apoptotic signaling pathway / RUNX2 regulates osteoblast differentiation / Fc-gamma receptor signaling pathway involved in phagocytosis / PECAM1 interactions / regulation of cell-cell adhesion / GRB2:SOS provides linkage to MAPK signaling for Integrins / progesterone receptor signaling pathway / RHOU GTPase cycle / Recycling pathway of L1 / positive regulation of epithelial cell migration / RET signaling / regulation of heart rate by cardiac conduction / FCGR activation / signaling receptor activator activity / negative regulation of anoikis / Long-term potentiation / EPH-ephrin mediated repulsion of cells / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / transforming growth factor beta receptor signaling pathway / GAB1 signalosome / negative regulation of hippo signaling / protein tyrosine kinase activator activity / T cell costimulation / Nuclear signaling by ERBB4 / lactation / osteoclast differentiation / negative regulation of protein-containing complex assembly / ephrin receptor binding / phospholipase binding / Signaling by ERBB2 / Integrin signaling / p38MAPK events / EPHB-mediated forward signaling / positive regulation of TORC1 signaling / peptidyl-tyrosine phosphorylation / NCAM signaling for neurite out-growth / Downstream signal transduction / FCGR3A-mediated IL10 synthesis / ionotropic glutamate receptor binding / positive regulation of glycolytic process / SH2 domain binding / integrin-mediated signaling pathway / response to interleukin-1 / negative regulation of extrinsic apoptotic signaling pathway / Downregulation of ERBB4 signaling / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / InlA-mediated entry of Listeria monocytogenes into host cells / angiotensin-activated signaling pathway
Similarity search - Function
: / 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 / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
Chem-L1N / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsZhu, S.J. / Bi, S.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81903539 China
CitationJournal: To Be Published
Title: The complex of Src with GW8510
Authors: Zhu, S.J. / Bi, S.Z.
History
DepositionOct 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Proto-oncogene tyrosine-protein kinase Src
B: Isoform 2 of Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4704
Polymers63,5712
Non-polymers8992
Water1,51384
1
A: Isoform 2 of Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2352
Polymers31,7861
Non-polymers4501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 2 of Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2352
Polymers31,7861
Non-polymers4501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.830, 62.580, 74.260
Angle α, β, γ (deg.)79.30, 87.98, 89.73
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Isoform 2 of Proto-oncogene tyrosine-protein kinase Src / Proto-oncogene c-Src / pp60c-src / p60-Src


Mass: 31785.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRC, SRC1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P12931, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-L1N / 4-[(~{E})-(7-oxidanyl-6~{H}-pyrrolo[2,3-g][1,3]benzothiazol-8-yl)methylideneamino]-~{N}-pyridin-2-yl-benzenesulfonamide


Mass: 449.506 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H15N5O3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3 Å3/Da / Density % sol: 59.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MOPS pH 7.0, 18% PEG 3350, 5% Glycerol, 5 mM TCEP

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.27→43.2 Å / Num. obs: 33316 / % possible obs: 97.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 37.83 Å2 / Rpim(I) all: 0.131 / Net I/σ(I): 4.4
Reflection shellResolution: 2.27→2.33 Å / Num. unique obs: 2502 / Rpim(I) all: 0.644

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BDF

2bdf


Resolution: 2.27→32.96 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 1677 5.03 %
Rwork0.2074 --
obs0.2095 33316 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→32.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3939 0 62 84 4085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.288
X-RAY DIFFRACTIONf_dihedral_angle_d8.176545
X-RAY DIFFRACTIONf_chiral_restr0.065594
X-RAY DIFFRACTIONf_plane_restr0.022705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.340.32681440.27472646X-RAY DIFFRACTION97
2.34-2.410.32541040.25532647X-RAY DIFFRACTION97
2.41-2.50.26451590.24892610X-RAY DIFFRACTION97
2.5-2.60.29141520.23462645X-RAY DIFFRACTION97
2.6-2.720.2831310.23372621X-RAY DIFFRACTION98
2.72-2.860.25381630.21472623X-RAY DIFFRACTION98
2.86-3.040.24291330.20992649X-RAY DIFFRACTION98
3.04-3.270.27031340.21912678X-RAY DIFFRACTION98
3.27-3.60.25941540.19622643X-RAY DIFFRACTION98
3.6-4.120.23191360.192660X-RAY DIFFRACTION98
4.12-5.190.19811590.18142610X-RAY DIFFRACTION97
5.19-32.960.26811080.20242607X-RAY DIFFRACTION96

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