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- PDB-7mow: PTP1B F225I in complex with TCS401 -

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Basic information

Entry
Database: PDB / ID: 7mow
TitlePTP1B F225I in complex with TCS401
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE / PROTEIN TYROSINE PHOSPHATASE
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 / negative regulation of MAP kinase activity / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / positive regulation of systemic arterial blood pressure / peptidyl-tyrosine dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / Regulation of IFNA/IFNB signaling / cellular response to angiotensin / regulation of proteolysis / 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 / ephrin receptor binding / MECP2 regulates neuronal receptors and channels / 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, 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 ...Protein-tyrosine phosphatase, non-receptor type-1/2 / : / 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
Similarity search - Domain/homology
Chem-OTA / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTorgeson, K.R. / Page, R. / Peti, W.
Funding support United States, 2items
OrganizationGrant numberCountry
American Diabetes Association1-14-ACN-31 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098482 United States
CitationJournal: Sci Adv / Year: 2022
Title: Conserved conformational dynamics determine enzyme activity.
Authors: Torgeson, K.R. / Clarkson, M.W. / Granata, D. / Lindorff-Larsen, K. / Page, R. / Peti, W.
History
DepositionMay 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,51710
Polymers35,7631
Non-polymers7549
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.609, 88.609, 103.571
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Tyrosine-protein phosphatase non-receptor type 1 / Protein-tyrosine phosphatase 1B / PTP-1B


Mass: 35762.730 Da / Num. of mol.: 1 / Mutation: F225I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Production host: Escherichia coli (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase

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Non-polymers , 5 types, 268 molecules

#2: Chemical ChemComp-OTA / 2-(OXALYL-AMINO)-4,5,6,7-TETRAHYDRO-THIENO[2,3-C]PYRIDINE-3-CARBOXYLIC ACID


Mass: 270.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N2O5S
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.28 Å3/Da / Density % sol: 62.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M MgCl2, 0.1 M Tris pH 8, 17.5% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.8→38.37 Å / Num. obs: 44140 / % possible obs: 99.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.078 / Net I/σ(I): 20.4
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.915 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2545 / CC1/2: 0.814

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHENIX1.19.1_4122phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5k9v

5k9v


Resolution: 1.8→38.37 Å / SU ML: 0.1906 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.7094
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1757 2402 5.45 %
Rwork0.1547 41682 -
obs0.1559 44084 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.61 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 43 259 2720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01772574
X-RAY DIFFRACTIONf_angle_d1.52813481
X-RAY DIFFRACTIONf_chiral_restr0.1105367
X-RAY DIFFRACTIONf_plane_restr0.0126452
X-RAY DIFFRACTIONf_dihedral_angle_d15.6425987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.26381490.2422374X-RAY DIFFRACTION98.82
1.84-1.880.25381470.21122426X-RAY DIFFRACTION100
1.88-1.920.18351340.17822439X-RAY DIFFRACTION99.88
1.92-1.970.18621550.16152420X-RAY DIFFRACTION100
1.97-2.020.1848970.15212439X-RAY DIFFRACTION99.8
2.02-2.080.21581430.16232417X-RAY DIFFRACTION99.96
2.08-2.150.18481410.16862429X-RAY DIFFRACTION100
2.15-2.220.20581300.14912470X-RAY DIFFRACTION99.96
2.22-2.310.16111560.14732416X-RAY DIFFRACTION99.96
2.31-2.420.16731310.15192437X-RAY DIFFRACTION100
2.42-2.550.17471310.15362454X-RAY DIFFRACTION100
2.55-2.710.20831570.15822426X-RAY DIFFRACTION100
2.71-2.910.18391380.16252463X-RAY DIFFRACTION100
2.91-3.210.17641500.16032478X-RAY DIFFRACTION100
3.21-3.670.18081490.14122474X-RAY DIFFRACTION100
3.67-4.620.1371440.132502X-RAY DIFFRACTION99.89
4.63-38.370.15881500.16232618X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: -36.8711600783 Å / Origin y: 30.2538435332 Å / Origin z: -14.7954027562 Å
111213212223313233
T0.114529779148 Å2-0.0247829796287 Å2-0.000161382916127 Å2-0.183487445217 Å20.0109734192669 Å2--0.118440326931 Å2
L1.63800249171 °2-0.142138313409 °2-0.144072858927 °2-1.45296314096 °20.373233518431 °2--1.33316125954 °2
S0.014054556631 Å °0.0270686935904 Å °0.00599386500534 Å °-0.00937181257045 Å °0.0138942582983 Å °0.000123554808658 Å °0.105012530894 Å °0.0127288917335 Å °-0.0245074580396 Å °
Refinement TLS groupSelection details: all

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