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- PDB-4i8n: CRYSTAL STRUCTURE of PROTEIN TYROSINE PHOSPHATASE 1B IN COMPLEX W... -

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Basic information

Entry
Database: PDB / ID: 4i8n
TitleCRYSTAL STRUCTURE of PROTEIN TYROSINE PHOSPHATASE 1B IN COMPLEX WITH AN INHIBITOR [(4-{(2S)-2-(1,3-BENZOXAZOL-2-YL)-2-[(4-FLUOROPHENYL)SULFAMOYL]ETHYL}PHENYL)AMINO](OXO)ACETIC ACID
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEIN PHOSPHATASE / PTP1B / HYDROLASE-HYDROLASE 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-1CG / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsReddy, S.M.V.V.V. / Rao, K.N. / Subramanya, H.
CitationJournal: Protein Pept.Lett. / Year: 2014
Title: X-Ray Structure of PTP1B in Complex with a New PTP1B Inhibitor.
Authors: Reddy, M.V. / Ghadiyaram, C. / Panigrahi, S.K. / Krishnamurthy, N.R. / Hosahalli, S. / Chandrasekharappa, A.P. / Manna, D. / Badiger, S.E. / Dubey, P.K. / Mangamoori, L.N.
History
DepositionDec 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2882
Polymers40,8041
Non-polymers4831
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.890, 87.890, 103.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 40804.449 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-1CG / [(4-{(2S)-2-(1,3-benzoxazol-2-yl)-2-[(4-fluorophenyl)sulfamoyl]ethyl}phenyl)amino](oxo)acetic acid


Mass: 483.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H18FN3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES PH 7.5, 19% PEG4000 and 10 % v/v 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.546 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 18, 2011 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.546 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 15530 / % possible obs: 93.7 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 10.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1519 / Rsym value: 0.407 / % possible all: 93.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.2.0001refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→27.74 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.089 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.356 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24753 782 5.1 %RANDOM
Rwork0.18447 ---
obs0.18759 14683 93.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.144 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→27.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 0 34 58 2526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222526
X-RAY DIFFRACTIONr_bond_other_d0.0020.022237
X-RAY DIFFRACTIONr_angle_refined_deg2.3351.973408
X-RAY DIFFRACTIONr_angle_other_deg1.01135230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5775297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4924.194124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.46815464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1711517
X-RAY DIFFRACTIONr_chiral_restr0.1250.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022770
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02521
X-RAY DIFFRACTIONr_nbd_refined0.2410.2578
X-RAY DIFFRACTIONr_nbd_other0.2120.22310
X-RAY DIFFRACTIONr_nbtor_other0.10.21442
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2105
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.22
X-RAY DIFFRACTIONr_mcbond_it1.4191.51866
X-RAY DIFFRACTIONr_mcbond_other0.2621.5600
X-RAY DIFFRACTIONr_mcangle_it1.79822407
X-RAY DIFFRACTIONr_scbond_it2.83631238
X-RAY DIFFRACTIONr_scangle_it4.1554.51001
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.379 56
Rwork0.258 1071

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