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- PDB-3zm1: Catalytic domain of human SHP2 -

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Basic information

Entry
Database: PDB / ID: 3zm1
TitleCatalytic domain of human SHP2
ComponentsTYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 11
KeywordsHYDROLASE / PTP1B
Function / homology
Function and homology information


atrioventricular canal development / genitalia development / STAT5 Activation / Co-inhibition by BTLA / Netrin mediated repulsion signals / negative regulation of neutrophil activation / positive regulation of lipopolysaccharide-mediated signaling pathway / Interleukin-37 signaling / Signaling by Leptin / negative regulation of cell adhesion mediated by integrin ...atrioventricular canal development / genitalia development / STAT5 Activation / Co-inhibition by BTLA / Netrin mediated repulsion signals / negative regulation of neutrophil activation / positive regulation of lipopolysaccharide-mediated signaling pathway / Interleukin-37 signaling / Signaling by Leptin / negative regulation of cell adhesion mediated by integrin / positive regulation of ossification / MET activates PTPN11 / negative regulation of chondrocyte differentiation / face morphogenesis / Regulation of RUNX1 Expression and Activity / Signal regulatory protein family interactions / ERBB signaling pathway / Interleukin-20 family signaling / Interleukin-6 signaling / Co-inhibition by CTLA4 / PI-3K cascade:FGFR3 / STAT5 activation downstream of FLT3 ITD mutants / Platelet sensitization by LDL / negative regulation of T cell activation / PI-3K cascade:FGFR2 / peptide hormone receptor binding / PI-3K cascade:FGFR4 / MAPK3 (ERK1) activation / negative regulation of type I interferon production / PI-3K cascade:FGFR1 / regulation of type I interferon-mediated signaling pathway / MAPK1 (ERK2) activation / inner ear development / Prolactin receptor signaling / PECAM1 interactions / peptidyl-tyrosine dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / fibroblast growth factor receptor signaling pathway / Regulation of IFNA/IFNB signaling / RET signaling / positive regulation of intracellular signal transduction / Interleukin-3, Interleukin-5 and GM-CSF signaling / Co-inhibition by PD-1 / PI3K Cascade / ephrin receptor signaling pathway / positive regulation of insulin receptor signaling pathway / regulation of protein-containing complex assembly / Regulation of IFNG signaling / GAB1 signalosome / negative regulation of T cell receptor signaling pathway / negative regulation of T cell proliferation / Activated NTRK2 signals through FRS2 and FRS3 / GPVI-mediated activation cascade / T cell costimulation / Signaling by CSF3 (G-CSF) / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / phosphotyrosine residue binding / FRS-mediated FGFR4 signaling / phosphoprotein phosphatase activity / FRS-mediated FGFR1 signaling / protein-tyrosine-phosphatase / Tie2 Signaling / FLT3 Signaling / protein tyrosine phosphatase activity / cell adhesion molecule binding / positive regulation of interferon-beta production / Downstream signal transduction / cellular response to epidermal growth factor stimulus / protein tyrosine kinase binding / positive regulation of D-glucose import across plasma membrane / insulin receptor binding / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Negative regulation of FGFR3 signaling / cellular response to mechanical stimulus / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / brain development / Signaling by SCF-KIT / Spry regulation of FGF signaling / receptor tyrosine kinase binding / vasodilation / epidermal growth factor receptor signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / cytokine-mediated signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / Interferon alpha/beta signaling / positive regulation of tumor necrosis factor production / PIP3 activates AKT signaling / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / signaling receptor complex adaptor activity / molecular adaptor activity / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cadherin binding / focal adhesion / protein kinase binding
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-6, -11 / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 11
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBohm, K. / Schuetz, A. / Roske, Y. / Heinemann, U.
CitationJournal: Chemmedchem / Year: 2015
Title: Selective Inhibitors of the Protein Tyrosine Phosphatase Shp2 Block Cellular Motility and Growth of Cancer Cells in Vitro and in Vivo.
Authors: Grosskopf, S. / Eckert, C. / Arkona, C. / Radetzki, S. / Bohm, K. / Heinemann, U. / Wolber, G. / Von Kries, J. / Birchmeier, W. / Rademann, J.
History
DepositionFeb 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 11


Theoretical massNumber of molelcules
Total (without water)33,1101
Polymers33,1101
Non-polymers00
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.174, 42.051, 49.256
Angle α, β, γ (deg.)72.00, 80.28, 74.19
Int Tables number1
Space group name H-MP1

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Components

#1: Protein TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 11 / PROTEIN-TYROSINE PHOSPHATASE 1D / PTP-1D / PROTEIN-TYROSINE PHOSPHATASE 2C / PTP-2C / SH-PTP2 / SHP- ...PROTEIN-TYROSINE PHOSPHATASE 1D / PTP-1D / PROTEIN-TYROSINE PHOSPHATASE 2C / PTP-2C / SH-PTP2 / SHP-2 / SHP2 / SH-PTP3


Mass: 33109.609 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 248-527
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PT7HT (MODIFIED PET) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): SCS1 ROSETTA T1R / References: UniProt: Q06124, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.29 Å3/Da / Density % sol: 46.29 % / Description: NONE
Crystal growDetails: 16-22% (W/V) PEG3350, 0.1-0.2 M SODIUM CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 48750 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 22.8
Reflection shellResolution: 1.4→1.48 Å / Mean I/σ(I) obs: 5.7 / % possible all: 49.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B7O

3b7o


Resolution: 1.4→19.12 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.912 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 255-262, 313-323, 408-411 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.20281 2494 5 %RANDOM
Rwork0.17023 ---
obs0.17188 47402 86.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20.14 Å2-0.08 Å2
2--0.15 Å20.15 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2118 0 0 283 2401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222216
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9353004
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4245271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50923.628113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78115401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5371518
X-RAY DIFFRACTIONr_chiral_restr0.0930.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021691
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21053
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21530
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2203
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.65621344
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.47132146
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4164.5990
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2556851
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.37432334
X-RAY DIFFRACTIONr_sphericity_free5.2823283
X-RAY DIFFRACTIONr_sphericity_bonded4.43332161
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 98 -
Rwork0.195 1877 -
obs--46.58 %

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