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- PDB-1nwl: Crystal structure of the PTP1B complexed with SP7343-SP7964, a pT... -

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Basic information

Entry
Database: PDB / ID: 1nwl
TitleCrystal structure of the PTP1B complexed with SP7343-SP7964, a pTyr mimetic
Componentsprotein-tyrosine phosphatase, non-receptor type 1
KeywordsHYDROLASE / protein-small molecule inhibitor complex
Function / homology
Function and homology information


PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of IRE1-mediated unfolded protein response / negative regulation of PERK-mediated unfolded protein response / IRE1-mediated unfolded protein response / regulation of intracellular protein transport ...PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of IRE1-mediated unfolded protein response / negative regulation of PERK-mediated unfolded protein response / IRE1-mediated unfolded protein response / regulation of intracellular protein transport / cytoplasmic side of endoplasmic reticulum membrane / sorting endosome / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / positive regulation of protein tyrosine kinase activity / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / cellular response to unfolded protein / regulation of signal transduction / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of signal transduction / Regulation of IFNG signaling / Growth hormone receptor signaling / MECP2 regulates neuronal receptors and channels / negative regulation of MAP kinase activity / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / protein dephosphorylation / ephrin receptor binding / Integrin signaling / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein phosphatase 2A binding / endosome lumen / insulin receptor binding / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / insulin receptor signaling pathway / actin cytoskeleton organization / early endosome / mitochondrial matrix / cadherin binding / protein kinase binding / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-1/2 / : / 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 ...Protein-tyrosine phosphatase, non-receptor type-1/2 / : / 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 / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-964 / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsErlanson, D.A. / McDowell, R.S. / He, M.M. / Randal, M. / Simmons, R.L. / Kung, J. / Waight, A. / Hansen, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Discovery of a New Phosphotyrosine Mimetic for PTP1B Using Breakaway Tethering
Authors: Erlanson, D.A. / McDowell, R.S. / He, M.M. / Randal, M. / Simmons, R.L. / Kung, J. / Waight, A. / Hansen, S.
History
DepositionFeb 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein-tyrosine phosphatase, non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1403
Polymers34,6461
Non-polymers4942
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.721, 88.721, 104.998
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

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Components

#1: Protein protein-tyrosine phosphatase, non-receptor type 1 / E.C.3.1.3.48 / PTP-1B / Protein-tyrosine phosphatase 1B / protein tyrosine phosphatase / placental


Mass: 34646.441 Da / Num. of mol.: 1 / Fragment: residues 1-298 / Mutation: R47C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-964 / 3-(4-{2-[2-(2-BROMO-ACETYLAMINO)-ETHYLDISULFANYL]-ETHYLCARBAMOYL}-CYCLOHEXYLCARBAMOYL)-PYRAZINE-2-CARBOXYLIC ACID / SP7343-SP7964


Mass: 469.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H27N5O5S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 3.4 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, magnesium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 %PEG80001reservoir
210 mMHEPES1reservoirpH7.4
3100 mM1reservoirMgOAc
450000 nmwater1reservoir

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Data collection

DiffractionMean temperature: 178 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 23, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 18095 / Num. obs: 18095 / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 2.4 Å / % possible obs: 98.1 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.48 Å / % possible obs: 98.1 % / Rmerge(I) obs: 0.175

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1.19refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.74 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24496 972 5.1 %RANDOM
Rwork0.20842 ---
obs0.21034 18095 99.82 %-
all-18095 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.25 Å20 Å2
2--0.51 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 38 167 2509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212394
X-RAY DIFFRACTIONr_angle_refined_deg0.921.973236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0415282
X-RAY DIFFRACTIONr_chiral_restr0.0580.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021797
X-RAY DIFFRACTIONr_nbd_refined0.1610.21085
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2178
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4880.216
X-RAY DIFFRACTIONr_mcbond_it1.6612.51412
X-RAY DIFFRACTIONr_mcangle_it2.99452287
X-RAY DIFFRACTIONr_scbond_it1.7482.5982
X-RAY DIFFRACTIONr_scangle_it2.7695944
LS refinement shellResolution: 2.4→2.483 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.341 84
Rwork0.241 1729
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.006
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg0.92
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.48 Å

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