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- PDB-1g7g: HUMAN PTP1B CATALYTIC DOMAIN COMPLEXES WITH PNU179326 -

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Basic information

Entry
Database: PDB / ID: 1g7g
TitleHUMAN PTP1B CATALYTIC DOMAIN COMPLEXES WITH PNU179326
ComponentsPROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1
KeywordsHYDROLASE / HYDROLASE (PHOSPHORYLASE) / 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-INX / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 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 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)35,3202
Polymers34,7211
Non-polymers6001
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.918, 82.443, 88.652
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: 34720.566 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-INX / 2-(CARBOXYMETHOXY)-5-[(2S)-2-({(2S)-2-[(3-CARBOXYPROPANOYL)AMINO] -3-PHENYLPROPANOYL}AMINO)-3-OXO-3-(PENTYLAMINO)PROPYL]BENZOIC ACID


Mass: 599.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H37N3O10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.78 Å3/Da / Density % sol: 55.82 %
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 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 12, 1997 / Details: MIRROR
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 17760 / Num. obs: 15251 / % possible obs: 87.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.264 / % possible all: 54.8
Reflection
*PLUS
Num. measured all: 249675
Reflection shell
*PLUS
Lowest resolution: 2.5 Å / % possible obs: 65.1 %

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Processing

Software
NameClassification
X-PLORmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PTP1B + 177496

Resolution: 2.2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.262 919 RANDOM
Rwork0.193 --
all0.212 17733 -
obs0.203 15245 -
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2427 0 43 109 2579
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d0.037
X-RAY DIFFRACTIONp_mcbond_it3.721
X-RAY DIFFRACTIONp_mcangle_it4.984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
2.2-2.310.33900.217X-RAY DIFFRACTION147758
2.31-2.4330.261020.194X-RAY DIFFRACTION167172
2.433-2.5680.291940.188X-RAY DIFFRACTION171081
2.568-2.720.281920.18X-RAY DIFFRACTION174392
2.72-2.8910.263890.178X-RAY DIFFRACTION163597
2.891-3.0850.247690.178X-RAY DIFFRACTION148798
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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