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- PDB-1is0: Crystal Structure of a Complex of the Src SH2 Domain with Conform... -

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Basic information

Entry
Database: PDB / ID: 1is0
TitleCrystal Structure of a Complex of the Src SH2 Domain with Conformationally Constrained Peptide Inhibitor
Components
  • AY0 GLU GLU ILE peptide
  • Tyrosine-protein kinase transforming protein SRC
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / conformationaly constrained INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


osteoclast development / extrinsic component of cytoplasmic side of plasma membrane / bone resorption / negative regulation of intrinsic apoptotic signaling pathway / progesterone receptor signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell adhesion ...osteoclast development / extrinsic component of cytoplasmic side of plasma membrane / bone resorption / negative regulation of intrinsic apoptotic signaling pathway / progesterone receptor signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell adhesion / innate immune response / signaling receptor binding / ATP binding
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
Ac-pTyr-Glu-Glu-Ile, pYEEI / Tyrosine-protein kinase transforming protein Src
Similarity search - Component
Biological speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDavidson, J.P. / Lubman, O. / Rose, T. / Waksman, G. / Martin, S.F.
CitationJournal: J.Am.Chem.Soc. / Year: 2002
Title: Calorimetric and structural studies of 1,2,3-trisubstituted cyclopropanes as conformationally constrained peptide inhibitors of Src SH2 domain binding.
Authors: Davidson, J.P. / Lubman, O. / Rose, T. / Waksman, G. / Martin, S.F.
History
DepositionNov 2, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase transforming protein SRC
B: Tyrosine-protein kinase transforming protein SRC
C: AY0 GLU GLU ILE peptide
D: AY0 GLU GLU ILE peptide


Theoretical massNumber of molelcules
Total (without water)25,7474
Polymers25,7474
Non-polymers00
Water2,594144
1
A: Tyrosine-protein kinase transforming protein SRC
C: AY0 GLU GLU ILE peptide


Theoretical massNumber of molelcules
Total (without water)12,8732
Polymers12,8732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-8 kcal/mol
Surface area6110 Å2
MethodPISA
2
B: Tyrosine-protein kinase transforming protein SRC
D: AY0 GLU GLU ILE peptide


Theoretical massNumber of molelcules
Total (without water)12,8732
Polymers12,8732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-5 kcal/mol
Surface area5950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.355, 56.501, 69.305
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: 12186.738 Da / Num. of mol.: 2 / Fragment: SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P00524, EC: 2.7.1.112
#2: Protein/peptide AY0 GLU GLU ILE peptide


Type: Peptide-like / Class: Inhibitor / Mass: 686.601 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / References: Ac-pTyr-Glu-Glu-Ile, pYEEI
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PEPTIDE INHIBITOR IS A CONFORMATIONALLY CONSTRAINED ANALOG OF A PHOSPHOTYROSINE-CONTAINING TETRAPEPTIDE
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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 53% MPD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140 mg/mlprotein1drop
250 %MPD1reservoir
30.1 MHEPES1reservoirpH8.0

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. obs: 18121 / % possible obs: 97 % / Num. measured all: 101439 / Rmerge(I) obs: 0.031
Reflection shell
*PLUS
% possible obs: 95.3 % / Rmerge(I) obs: 0.11

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→22.32 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 578161.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1770 9.9 %RANDOM
Rwork0.236 ---
obs0.236 17894 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.8679 Å2 / ksol: 0.371906 e/Å3
Displacement parametersBiso mean: 22.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-6 Å
Luzzati sigma a0.22 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→22.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1724 0 0 144 1868
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.73
X-RAY DIFFRACTIONc_mcbond_it1.971.5
X-RAY DIFFRACTIONc_mcangle_it2.782
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.411 308 10.9 %
Rwork0.376 2521 -
obs--92.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_PTYR_PTR3.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3WATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 16124 / σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.267
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.73
X-RAY DIFFRACTIONc_mcbond_it1.971.5
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_mcangle_it2.782
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.411 / % reflection Rfree: 10.9 % / Rfactor Rwork: 0.376

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