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- PDB-2ptk: CHICKEN SRC TYROSINE KINASE -

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Basic information

Entry
Database: PDB / ID: 2ptk
TitleCHICKEN SRC TYROSINE KINASE
ComponentsTYROSINE-PROTEIN KINASE TRANSFORMING PROTEIN SRC
KeywordsTYROSINE-PROTEIN KINASE / SRC / SH2 / SH3
Function / homology
Function and homology information


Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / RAF activation / PIP3 activates AKT signaling / EPH-ephrin mediated repulsion of cells / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Activated NTRK3 signals through PI3K / Downstream signal transduction / Downregulation of ERBB4 signaling / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / DCC mediated attractive signaling / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / negative regulation of intrinsic apoptotic signaling pathway / progesterone receptor signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / epidermal growth factor receptor signaling pathway / cell junction / cell-cell junction / protein tyrosine kinase activity / protein phosphatase binding / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / cell differentiation / mitochondrial inner membrane / cytoskeleton / regulation of cell cycle / cell adhesion / endosome membrane / signaling receptor binding / innate immune response / focal adhesion / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / nucleus / membrane / plasma membrane / cytosol
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 / Src homology 3 domains ...SH2 domain / SHC Adaptor Protein / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH3 type barrels. / 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
Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsWilliams, J.C. / Wierenga, R.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: The 2.35 A crystal structure of the inactivated form of chicken Src: a dynamic molecule with multiple regulatory interactions
Authors: Williams, J.C. / Weijland, A. / Gonfloni, S. / Thompson, A. / Courtneidge, S.A. / Superti-Furga, G. / Wierenga, R.K.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Src Regulated by C-Terminal Phosphorylation is Monomeric
Authors: Weijland, A. / Williams, J.C. / Neubauer, G. / Courtneidge, S.A. / Wierenga, R.K. / Superti-Furga, G.
History
DepositionJun 17, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 11, 2018Group: Data collection / Other / Category: pdbx_database_status / Item: _pdbx_database_status.process_site
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYROSINE-PROTEIN KINASE TRANSFORMING PROTEIN SRC


Theoretical massNumber of molelcules
Total (without water)51,7341
Polymers51,7341
Non-polymers00
Water4,882271
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.561, 89.252, 97.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TYROSINE-PROTEIN KINASE TRANSFORMING PROTEIN SRC / SRC


Mass: 51733.551 Da / Num. of mol.: 1 / Fragment: SH3/SH2/KINASE/C-TERMINAL TAIL
Source method: isolated from a genetically manipulated source
Details: INACTIVE FORM, PHOSPHORYLATED AT TYR 527 / Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P00523, EC: 2.7.1.112
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.2 Å3/Da / Density % sol: 45 %
Crystal growpH: 8.2
Details: 16% PEG-2000 10% PEG-400 100MM TRIS PH=8.2 300MM NACL 1MM EDTA 1MM DTT 1MM AZIDE
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116-18 %PEG200011
210 %PEG40011
3100 mMTris-HCl11
4300 mM11NaCl
51 mMEDTA11
61 mMsodium azide11
71 mMreduced dithiothreitol11

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BL19 / Wavelength: 0.948
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 17, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 2.35→15 Å / Num. obs: 19579 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 22
Reflection shellResolution: 2.35→2.4 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.3 / % possible all: 98.8
Reflection
*PLUS
Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 5.1

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→5 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAIN / Cross valid method: THROUGHOUT / σ(F): 2.5
Details: WEAK DENSITY OBSERVED FOR RESIDUES 210 - 212, 300 - 305, 407 - 424, 529 - 533. WEAK DENSITY OBSERVED FOR RESIDUES 210 - 212, 300 - 305, 407 - 424, 529 - 533.
RfactorNum. reflection% reflectionSelection details
Rfree0.292 804 10 %RANDOM
Rwork0.204 ---
obs0.204 14735 85 %-
Displacement parametersBiso mean: 53 Å2
Baniso -1Baniso -2Baniso -3
1--14.3416 Å20 Å20 Å2
2--6.1454 Å20 Å2
3---8.1962 Å2
Refinement stepCycle: LAST / Resolution: 2.35→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 0 275 3702
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.4
X-RAY DIFFRACTIONx_mcangle_it5.1
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.35→2.44 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3615 81 4.5 %
Rwork0.3323 1568 -
obs--89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPARAM19.SOL
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.3323

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