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- PDB-1a09: C-src (SH2 domain) complexed with ace-formyl phosphotyr-glu-(n,n-... -

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Basic information

Entry
Database: PDB / ID: 1a09
TitleC-src (SH2 domain) complexed with ace-formyl phosphotyr-glu-(n,n-dipentyl amine)
Components
  • ACE-FORMYL PHOSPHOTYR-GLU-(N,N-DIPENTYL AMINE)
  • C-SRC TYROSINE KINASE
KeywordsCOMPLEX (TRANSFERASE/PEPTIDE) / COMPLEX (TRANSFERASE-PEPTIDE) / COMPLEX (TRANSFERASE-PEPTIDE) complex
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 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...SH2 domain / SHC Adaptor Protein / : / 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 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShewchuk, L. / Jordan, S.
CitationJournal: Biochemistry / Year: 1997
Title: Peptide ligands of pp60(c-src) SH2 domains: a thermodynamic and structural study.
Authors: Charifson, P.S. / Shewchuk, L.M. / Rocque, W. / Hummel, C.W. / Jordan, S.R. / Mohr, C. / Pacofsky, G.J. / Peel, M.R. / Rodriguez, M. / Sternbach, D.D. / Consler, T.G.
History
DepositionDec 10, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-SRC TYROSINE KINASE
C: ACE-FORMYL PHOSPHOTYR-GLU-(N,N-DIPENTYL AMINE)
B: C-SRC TYROSINE KINASE
D: ACE-FORMYL PHOSPHOTYR-GLU-(N,N-DIPENTYL AMINE)


Theoretical massNumber of molelcules
Total (without water)25,7794
Polymers25,7794
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: C-SRC TYROSINE KINASE
C: ACE-FORMYL PHOSPHOTYR-GLU-(N,N-DIPENTYL AMINE)


Theoretical massNumber of molelcules
Total (without water)12,8902
Polymers12,8902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint0.1 kcal/mol
Surface area6160 Å2
MethodPISA
3
B: C-SRC TYROSINE KINASE
D: ACE-FORMYL PHOSPHOTYR-GLU-(N,N-DIPENTYL AMINE)


Theoretical massNumber of molelcules
Total (without water)12,8902
Polymers12,8902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-0.9 kcal/mol
Surface area5990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.900, 66.000, 74.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8073, 0.2971, -0.5099), (0.2697, 0.9543, 0.1291), (0.525, -0.0334, -0.8505)
Vector: 97.6861, -0.9095, 32.2239)

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Components

#1: Protein C-SRC TYROSINE KINASE


Mass: 12303.886 Da / Num. of mol.: 2 / Fragment: SH2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Gene: SRC / Plasmid: PET11B / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): SRC / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P12931, EC: 2.7.1.112
#2: Protein/peptide ACE-FORMYL PHOSPHOTYR-GLU-(N,N-DIPENTYL AMINE)


Mass: 585.626 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / pH: 4.6
Details: PROTEIN WAS CRYSTALLIZED FROM 0.1 M ACETATE, PH 4.6, 2 M NAFORMATE AT 4 C. THE CRYSTAL WAS SOAKED IN 10% PEG400, 10% GLYCEROL PRIOR TO DATA COLLECTION, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1125 mg/mlprotein1drop
220 mMHEPES1drop
3350 mM1dropNaCl
45 mMdithiothreitol1drop
55 mMEDTA1drop
60.1 Macetate1reservoir
72 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1993 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 17257 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.3
Reflection shellResolution: 2→2.2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 4.4 / % possible all: 93.6

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
R-AXISdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SHD

1shd


Resolution: 2→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / σ(F): 2 / Details: PARTIALLY REFINED
RfactorNum. reflection% reflection
Rwork0.198 --
obs0.198 17233 96 %
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1658 0 82 193 1933
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.667
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.65
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.531
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2→2.2 Å / Total num. of bins used: 8 / % reflection obs: 91.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19.PTATOPH19.PTA
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.65
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.531

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