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- PDB-1g7f: HUMAN PTP1B CATALYTIC DOMAIN COMPLEXED WITH PNU177496 -

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Basic information

Entry
Database: PDB / ID: 1g7f
TitleHUMAN PTP1B CATALYTIC DOMAIN COMPLEXED WITH PNU177496
ComponentsPROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1
KeywordsHYDROLASE / HYDROLASE (PHOSPHORYLATION) / TYROSINE PHOSPHATASE / 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 / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / positive regulation of protein tyrosine kinase activity / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome ...PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / positive regulation of protein tyrosine kinase activity / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / negative regulation of vascular associated smooth muscle cell migration / mitochondrial crista / cytoplasmic side of endoplasmic reticulum membrane / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / negative regulation of PERK-mediated unfolded protein response / positive regulation of JUN kinase activity / positive regulation of systemic arterial blood pressure / negative regulation of MAP kinase activity / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / peptidyl-tyrosine dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / Regulation of IFNA/IFNB signaling / regulation of proteolysis / cellular response to angiotensin / regulation of postsynapse assembly / positive regulation of endothelial cell apoptotic process / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of cell-substrate adhesion / cellular response to unfolded protein / regulation of signal transduction / Regulation of IFNG signaling / negative regulation of signal transduction / Growth hormone receptor signaling / positive regulation of cardiac muscle cell apoptotic process / positive regulation of heart rate / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein dephosphorylation / endoplasmic reticulum unfolded protein response / MECP2 regulates neuronal receptors and channels / ephrin receptor binding / Insulin receptor recycling / cellular response to platelet-derived growth factor stimulus / cellular response to fibroblast growth factor stimulus / Integrin signaling / protein-tyrosine-phosphatase / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to nitric oxide / negative regulation of insulin receptor signaling pathway / protein tyrosine phosphatase activity / protein phosphatase 2A binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / endosome lumen / insulin receptor binding / response to nutrient levels / Negative regulation of MET activity / cellular response to nerve growth factor stimulus / receptor tyrosine kinase binding / negative regulation of ERK1 and ERK2 cascade / insulin receptor signaling pathway / negative regulation of neuron projection development / actin cytoskeleton organization / cellular response to hypoxia / early endosome / postsynapse / cadherin binding / mitochondrial matrix / negative regulation of cell population proliferation / protein kinase binding / glutamatergic synapse / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytoplasm / cytosol
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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-INZ / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBleasdale, J.E. / Ogg, D. / Larsen, S.D.
CitationJournal: Biochemistry / Year: 2001
Title: Small molecule peptidomimetics containing a novel phosphotyrosine bioisostere inhibit protein tyrosine phosphatase 1B and augment insulin action.
Authors: Bleasdale, J.E. / Ogg, D. / Palazuk, B.J. / Jacob, C.S. / Swanson, M.L. / Wang, X.Y. / Thompson, D.P. / Conradi, R.A. / Mathews, W.R. / Laborde, A.L. / Stuchly, C.W. / Heijbel, A. / ...Authors: Bleasdale, J.E. / Ogg, D. / Palazuk, B.J. / Jacob, C.S. / Swanson, M.L. / Wang, X.Y. / Thompson, D.P. / Conradi, R.A. / Mathews, W.R. / Laborde, A.L. / Stuchly, C.W. / Heijbel, A. / Bergdahl, K. / Bannow, C.A. / Smith, C.W. / Svensson, C. / Liljebris, C. / Schostarez, H.J. / May, P.D. / Stevens, F.C. / Larsen, S.D.
History
DepositionNov 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2502
Polymers34,7071
Non-polymers5441
Water8,323462
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.74, 83.82, 88.66
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 PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1 / PROTEIN-TYROSINE PHOSPHATASE 1B


Mass: 34706.539 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN (RESIDUES 1-298)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical ChemComp-INZ / 2-{4-[(2S)-2-[({[(1S)-1-CARBOXY-2-PHENYLETHYL]AMINO}CARBONYL)AMINO]-3-OXO-3-(PENTYLAMINO)PROPYL]PHENOXY}MALONIC ACID


Mass: 543.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N3O9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG8000, magnesium acetate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
225 mMTris1drop
30.3 M1dropNaCl
43 mMdithiothreitol1drop
55 mMEDTA1drop
65 mMinhibitor1drop
714-20 %PEG80001reservoir
80.2 Mmagnesium acetate1reservoir
90.1 Mcacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9765 Å
DetectorType: SIEMENS / Detector: CCD / Date: Oct 27, 1997
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 37591 / Num. obs: 36586 / % possible obs: 97.33 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.79 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.74 % / Rmerge(I) obs: 0.348 / % possible all: 97.33
Reflection
*PLUS
Num. measured all: 643419
Reflection shell
*PLUS
% possible obs: 97 %

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Processing

Software
NameClassification
MERLOTphasing
REFMACrefinement
SMARTdata reduction
SAINTdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ptv

1ptv


Resolution: 1.8→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.249 1824 RANDOM
Rwork0.18 --
all0.187 33641 -
obs0.188 32023 -
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 39 462 2927
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d0.024
X-RAY DIFFRACTIONp_mcbond_it1.901
X-RAY DIFFRACTIONp_mcangle_it2.695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.8-1.8910.3172510.248X-RAY DIFFRACTION418886
1.891-1.9920.242230.198X-RAY DIFFRACTION411194
1.992-2.1040.2272050.183X-RAY DIFFRACTION378396
2.104-2.230.2271680.173X-RAY DIFFRACTION337697
2.23-2.3720.231690.171X-RAY DIFFRACTION304898
2.372-2.5320.2261400.167X-RAY DIFFRACTION269298
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / σ(F): 0 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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