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- PDB-1ayd: CRYSTAL STRUCTURES OF PEPTIDE COMPLEXES OF THE AMINO-TERMINAL SH2... -

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Basic information

Entry
Database: PDB / ID: 1ayd
TitleCRYSTAL STRUCTURES OF PEPTIDE COMPLEXES OF THE AMINO-TERMINAL SH2 DOMAIN OF THE SYP TYROSINE PHOSPHATASE
ComponentsPROTEIN-TYROSINE PHOSPHATASE SYP (N-TERMINAL SH2 DOMAIN)
KeywordsHYDROLASE(SH2 DOMAIN)
Function / homology
Function and homology information


PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / MET activates PTPN11 / Regulation of IFNA/IFNB signaling / Costimulation by the CD28 family / FRS-mediated FGFR1 signaling ...PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / MET activates PTPN11 / Regulation of IFNA/IFNB signaling / Costimulation by the CD28 family / FRS-mediated FGFR1 signaling / FRS-mediated FGFR2 signaling / Tie2 Signaling / PECAM1 interactions / Interleukin-20 family signaling / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Signaling by CSF3 (G-CSF) / CTLA4 inhibitory signaling / GAB1 signalosome / PI3K Cascade / Regulation of RUNX1 Expression and Activity / Interleukin-6 signaling / GPVI-mediated activation cascade / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Downstream signal transduction / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Spry regulation of FGF signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / PD-1 signaling / Signaling by SCF-KIT / positive regulation of signal transduction / negative regulation of hormone secretion / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / PIP3 activates AKT signaling / genitalia development / Platelet sensitization by LDL / atrioventricular canal development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / negative regulation of cell adhesion mediated by integrin / Interleukin-3, Interleukin-5 and GM-CSF signaling / RET signaling / positive regulation of hormone secretion / cerebellar cortex formation / multicellular organismal reproductive process / regulation of protein export from nucleus / positive regulation of ossification / hormone metabolic process / negative regulation of chondrocyte differentiation / triglyceride metabolic process / face morphogenesis / ERBB signaling pathway / peptide hormone receptor binding / platelet formation / negative regulation of type I interferon production / megakaryocyte development / organ growth / positive regulation of focal adhesion assembly / plasma membrane raft / inner ear development / phosphoprotein phosphatase activity / phospholipase binding / regulation of MAPK cascade / regulation of cell adhesion mediated by integrin / neurotrophin TRK receptor signaling pathway / Bergmann glial cell differentiation / platelet-derived growth factor receptor signaling pathway / non-membrane spanning protein tyrosine phosphatase activity / regulation of protein-containing complex assembly / peptidyl-tyrosine dephosphorylation / insulin receptor substrate binding / D1 dopamine receptor binding / negative regulation of insulin secretion / ephrin receptor signaling pathway / fibroblast growth factor receptor signaling pathway / positive regulation of insulin receptor signaling pathway / homeostasis of number of cells within a tissue / cellular response to epidermal growth factor stimulus / protein tyrosine kinase binding / positive regulation of interferon-beta production / cell adhesion molecule binding / hormone-mediated signaling pathway / phosphotyrosine residue binding / positive regulation of mitotic cell cycle / axonogenesis / protein-tyrosine-phosphatase / DNA damage checkpoint signaling / protein tyrosine phosphatase activity / integrin-mediated signaling pathway / positive regulation of glucose import / brain development / multicellular organism growth / insulin receptor binding / epidermal growth factor receptor signaling pathway / lipid metabolic process / receptor tyrosine kinase binding
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-6, -11 / SH2 domain / SHC Adaptor Protein / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. ...Protein-tyrosine phosphatase, non-receptor type-6, -11 / SH2 domain / SHC Adaptor Protein / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 11
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsLee, C.-H. / Kuriyan, J.
Citation
Journal: Structure / Year: 1994
Title: Crystal structures of peptide complexes of the amino-terminal SH2 domain of the Syp tyrosine phosphatase.
Authors: Lee, C.H. / Kominos, D. / Jacques, S. / Margolis, B. / Schlessinger, J. / Shoelson, S.E. / Kuriyan, J.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: Binding of a High Affinity Phosphotyrosyl Peptide to the Src Sh2 Domain: Crystal Structures of the Complexed and Peptide-Free Forms
Authors: Waksman, G. / Shoelson, S.E. / Pant, N. / Cowburn, D. / Kuriyan, J.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 1993
Title: Structures of Sh2 and SH3 Domains
Authors: Kuriyan, J. / Cowburn, D.
#3: Journal: Nature / Year: 1992
Title: Crystal Structure of the Phosphotyrosine Recognition Domain Sh2 of V-Src Complexed with Tyrosine-Phosphorylated Peptides
Authors: Waksman, G. / Kominos, D. / Robertson, S.R. / Pant, N. / Baltimore, D. / Birge, R.B. / Cowburn, D. / Hanafusa, H. / Mayer, B.J. / Overduin, M. / Resh, M.D. / Rios, C.B. / Silverman, L. / Kuriyan, J.
History
DepositionMay 15, 1994Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN-TYROSINE PHOSPHATASE SYP (N-TERMINAL SH2 DOMAIN)


Theoretical massNumber of molelcules
Total (without water)11,5291
Polymers11,5291
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.200, 63.200, 76.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN-TYROSINE PHOSPHATASE SYP (N-TERMINAL SH2 DOMAIN)


Mass: 11528.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P35235, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.66 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 %satammonium sulfate1reservoir
2100 mMMES1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / Num. obs: 8075 / % possible obs: 97 % / Num. measured all: 63420 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.24 Å / % possible obs: 92.1 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.2 -
obs0.2 6359
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms784 0 0 87 871
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg3
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3

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