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- PDB-1ksw: Structure of Human c-Src Tyrosine Kinase (Thr338Gly Mutant) in Co... -

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Basic information

Entry
Database: PDB / ID: 1ksw
TitleStructure of Human c-Src Tyrosine Kinase (Thr338Gly Mutant) in Complex with N6-benzyl ADP
ComponentsPROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC
KeywordsTRANSFERASE / SH3 / SH2 / Kinase / bump hole / bump-hole / chemical genetics / orthogonal substrate / ATP
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / cellular response to progesterone stimulus / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of dephosphorylation / regulation of cell projection assembly / negative regulation of telomere maintenance / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / ERBB2 signaling pathway ...regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / cellular response to progesterone stimulus / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of dephosphorylation / regulation of cell projection assembly / negative regulation of telomere maintenance / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / ERBB2 signaling pathway / Regulation of gap junction activity / negative regulation of focal adhesion assembly / BMP receptor binding / positive regulation of integrin activation / positive regulation of protein processing / Activated NTRK2 signals through FYN / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / negative regulation of neutrophil activation / regulation of vascular permeability / focal adhesion assembly / connexin binding / osteoclast development / Activated NTRK3 signals through PI3K / cellular response to fluid shear stress / signal complex assembly / positive regulation of small GTPase mediated signal transduction / branching involved in mammary gland duct morphogenesis / Co-stimulation by CD28 / Regulation of RUNX1 Expression and Activity / DCC mediated attractive signaling / EPH-Ephrin signaling / positive regulation of podosome assembly / positive regulation of lamellipodium morphogenesis / regulation of bone resorption / Ephrin signaling / Signal regulatory protein family interactions / odontogenesis / negative regulation of mitochondrial depolarization / podosome / MET activates PTK2 signaling / cellular response to peptide hormone stimulus / Regulation of KIT signaling / regulation of early endosome to late endosome transport / Signaling by ALK / leukocyte migration / phospholipase activator activity / oogenesis / Co-inhibition by CTLA4 / GP1b-IX-V activation signalling / EPHA-mediated growth cone collapse / Receptor Mediated Mitophagy / p130Cas linkage to MAPK signaling for integrins / interleukin-6-mediated signaling pathway / stress fiber assembly / positive regulation of Notch signaling pathway / Signaling by EGFR / RUNX2 regulates osteoblast differentiation / stimulatory C-type lectin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / forebrain development / regulation of cell-cell adhesion / uterus development / PECAM1 interactions / Recycling pathway of L1 / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of heart rate by cardiac conduction / RHOU GTPase cycle / protein tyrosine kinase activator activity / RET signaling / signaling receptor activator activity / negative regulation of anoikis / FCGR activation / Long-term potentiation / positive regulation of epithelial cell migration / progesterone receptor signaling pathway / positive regulation of protein serine/threonine kinase activity / EPH-ephrin mediated repulsion of cells / GAB1 signalosome / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / negative regulation of hippo signaling / bone resorption / negative regulation of protein-containing complex assembly / Nuclear signaling by ERBB4 / phospholipase binding / ephrin receptor binding / T cell costimulation / p38MAPK events / cellular response to platelet-derived growth factor stimulus / Signaling by ERBB2 / Integrin signaling / EPHB-mediated forward signaling / ionotropic glutamate receptor binding / positive regulation of TORC1 signaling / NCAM signaling for neurite out-growth / Downregulation of ERBB4 signaling / Downstream signal transduction
Similarity search - Function
SH2 domain / SHC Adaptor Protein / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. ...SH2 domain / SHC Adaptor Protein / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N6-BENZYL ADENOSINE-5'-DIPHOSPHATE / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWitucki, L.A. / Huang, X. / Shah, K. / Liu, Y. / Kyin, S. / Eck, M.J. / Shokat, K.M.
CitationJournal: Chem.Biol. / Year: 2002
Title: Mutant tyrosine kinases with unnatural nucleotide specificity retain the structure and phospho-acceptor specificity of the wild-type enzyme.
Authors: Witucki, L.A. / Huang, X. / Shah, K. / Liu, Y. / Kyin, S. / Eck, M.J. / Shokat, K.M.
History
DepositionJan 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1832
Polymers51,6661
Non-polymers5171
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.81, 87.68, 106.28
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC / C-SRC


Mass: 51665.520 Da / Num. of mol.: 1 / Fragment: SH3, SH2 and Kinase domains / Mutation: T338G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12931, EC: 2.7.1.112
#2: Chemical ChemComp-NBS / N6-BENZYL ADENOSINE-5'-DIPHOSPHATE


Mass: 517.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N5O10P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 4000, 50mM PIPES pH 6.5, 10mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110-15 mg/mlprotein1drop
220 mMHEPES1droppH7.6
3100 mM1dropNaCl
410 mMdithiothreitol1drop
51 mMN6-(benzyl)ADP1drop
650 mMPIPES1reservoirpH6.5
712 %PEG40001reservoir
810 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.917 Å
DetectorType: PRINCETON 2K / Detector: CCD / Date: Sep 16, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 12715 / Num. obs: 12715 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.071
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. measured all: 46549 / Rmerge(I) obs: 0.071

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2SRC

2src


Resolution: 2.8→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.294 -random 5%
Rwork0.231 --
all-12715 -
obs-12715 -
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3611 0 34 46 3691
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.771
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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