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- PDB-7klx: Protein Tyrosine Phosphatase 1B with inhibitor -

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Basic information

Entry
Database: PDB / ID: 7klx
TitleProtein Tyrosine Phosphatase 1B with inhibitor
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / insulin / regulation / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane ...regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / mitochondrial crista / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / non-membrane spanning protein tyrosine phosphatase activity / positive regulation of protein tyrosine kinase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / 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 / MECP2 regulates neuronal receptors and channels / Growth hormone receptor signaling / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / Insulin receptor recycling / negative regulation of insulin receptor signaling pathway / ephrin receptor binding / Integrin signaling / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of MAP kinase activity / protein phosphatase 2A binding / protein tyrosine phosphatase activity / 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 / 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 / Tyrosine-specific protein phosphatases domain ...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 / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
Chem-WOV / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.839 Å
AuthorsBattaile, K.P. / Chirgadze, Y. / Ruzanov, M. / Romanov, V. / Lam, K. / Gordon, R. / Lin, A. / Lam, R. / Pai, E. / Chirgadze, N.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2021
Title: Signal transfer in human protein tyrosine phosphatase PTP1B from allosteric inhibitor P00058.
Authors: Chirgadze, Y.N. / Battaile, K.P. / Likhachev, I.V. / Balabaev, N.K. / Gordon, R.D. / Romanov, V. / Lin, A. / Karisch, R. / Lam, R. / Ruzanov, M. / Brazhnikov, E.V. / Pai, E.F. / Neel, B.G. / Chirgadze, N.Y.
History
DepositionNov 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,0583
Polymers32,8031
Non-polymers2562
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.3, 88.3, 104.791
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 32802.574 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-WOV / 2-(2,5-dimethyl-1H-pyrrol-1-yl)-5-hydroxybenzoic acid


Mass: 231.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.6 Å3/Da / Density % sol: 65.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7 / Details: 12% PEG 3350, 100 mM magnesium acetate, 3% ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.84→76.47 Å / Num. obs: 40080 / % possible obs: 96.5 % / Redundancy: 10.9 % / CC1/2: 1 / Rpim(I) all: 0.016 / Net I/σ(I): 26.1
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2033 / CC1/2: 0.811 / Rpim(I) all: 0.325 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSJan 31, 2020data reduction
Aimless0.7.4data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CM8

2cm8


Resolution: 1.839→76.47 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.104 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.105 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.094
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 2012 -RANDOM
Rwork0.1962 ---
obs0.1967 40071 96.4 %-
Displacement parametersBiso mean: 40.15 Å2
Baniso -1Baniso -2Baniso -3
1--1.3426 Å20 Å20 Å2
2---1.3426 Å20 Å2
3---2.6851 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.839→76.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 18 118 2321
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082398HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.953269HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d839SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes434HARMONIC5
X-RAY DIFFRACTIONt_it2398HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion314SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies13HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact2160SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion15.73
LS refinement shellResolution: 1.84→1.85 Å
RfactorNum. reflection% reflection
Rfree0.2254 51 -
Rwork0.2117 --
obs0.2125 802 96.36 %
Refinement TLS params.Origin x: 42.8511 Å / Origin y: 16.4392 Å / Origin z: 15.3034 Å
111213212223313233
T0.0453 Å20.0769 Å2-0.0097 Å2--0.047 Å20.0001 Å2---0.0479 Å2
L1.3033 °2-0.3708 °20.6397 °2-0.7871 °2-0.1926 °2--1.5638 °2
S0.025 Å °0.0467 Å °0.0069 Å °0.0467 Å °0.0014 Å °0.1892 Å °0.0069 Å °0.1892 Å °-0.0264 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A4 - 281
2X-RAY DIFFRACTION1{ A|* }A401

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