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- PDB-1jf7: HUMAN PTP1B CATALYTIC DOMAIN COMPLEXED WITH PNU177836 -

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Basic information

Entry
Database: PDB / ID: 1jf7
TitleHUMAN PTP1B CATALYTIC DOMAIN COMPLEXED WITH PNU177836
ComponentsPROTEIN-TYROSINE PHOSPHATASE 1B
KeywordsHYDROLASE / HYDROLASE (PHOSPHORYLATION) / TYROSINE PHOSPHATASE / 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 / sorting endosome / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / 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 / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / positive regulation of protein tyrosine kinase activity / 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 / endoplasmic reticulum unfolded protein response / Growth hormone receptor signaling / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / ephrin receptor binding / Integrin signaling / protein dephosphorylation / negative regulation of MAP kinase activity / protein-tyrosine-phosphatase / 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 / 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 / Tyrosine specific protein phosphatases active site. ...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-TBH / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLarsen, S.D. / Barf, T. / Liljebris, C. / May, P.D. / Ogg, D. / O'Sullivan, T.J. / Palazuk, B.J. / Schostarez, H.J. / Stevens, F.C. / Bleasdale, J.E.
CitationJournal: J.Med.Chem. / Year: 2002
Title: Synthesis and biological activity of a novel class of small molecular weight peptidomimetic competitive inhibitors of protein tyrosine phosphatase 1B.
Authors: Larsen, S.D. / Barf, T. / Liljebris, C. / May, P.D. / Ogg, D. / O'Sullivan, T.J. / Palazuk, B.J. / Schostarez, H.J. / Stevens, F.C. / Bleasdale, J.E.
History
DepositionJun 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN-TYROSINE PHOSPHATASE 1B
B: PROTEIN-TYROSINE PHOSPHATASE 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0473
Polymers69,4412
Non-polymers6061
Water6,431357
1
A: PROTEIN-TYROSINE PHOSPHATASE 1B


Theoretical massNumber of molelcules
Total (without water)34,7211
Polymers34,7211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN-TYROSINE PHOSPHATASE 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3262
Polymers34,7211
Non-polymers6061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.595, 88.266, 65.786
Angle α, β, γ (deg.)90.00, 107.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN-TYROSINE PHOSPHATASE 1B / PTP-1B


Mass: 34720.566 Da / Num. of mol.: 2 / Fragment: Catalytic Domain
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-TBH / 5-(2-{2-[(TERT-BUTOXY-HYDROXY-METHYL)-AMINO]-1-HYDROXY-3-PHENYL-PROPYLAMINO}-3-HYDROXY-3-PENTYLAMINO-PROPYL)-2-CARBOXYMETHOXY-BENZOIC ACID / PNU177836


Mass: 605.720 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H47N3O9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG6000, ammonium sulphate, glycerol, Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
225 mMTris1droppH7.5
30.3 M1dropNaCl
43 mMdithiothreitol1drop
55 mMEDTA1drop
65 mMinhibitor1drop
714-20 %PEG60001reservoir
80.2 Mammonium sulfate1reservoir
90.1 MHEPES1reservoirpH8.0
1012 %glycerol1reservoir

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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: Dec 10, 1997
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: 33693 / Num. obs: 32150 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 37.587 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 19.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.89 % / Rmerge(I) obs: 0.177 / % possible all: 89.9
Reflection
*PLUS
Num. obs: 33693 / Num. measured all: 537079
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 89.9 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PTV

1ptv


Resolution: 2.2→15 Å / SU B: 7.398 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.32 / ESU R Free: 0.247 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26751 1628 5.1 %RANDOM
Rwork0.20267 ---
obs0.20607 30373 95.49 %-
all-33627 --
Displacement parametersBiso mean: 36.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20 Å2-2.85 Å2
2---1.67 Å20 Å2
3----1.77 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4592 0 43 357 4992
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_mcbond_it0.971.5
X-RAY DIFFRACTIONp_mcangle_it1.8062
X-RAY DIFFRACTIONp_scbond_it2.8123
X-RAY DIFFRACTIONp_scangle_it4.4284.5
X-RAY DIFFRACTIONp_bond_d0.0170.021
X-RAY DIFFRACTIONp_angle_d1.8071.96
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 87 4.3 %
Rwork0.212 2033 -
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.95 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_mcbond_it1.5
X-RAY DIFFRACTIONp_scbond_it3
X-RAY DIFFRACTIONp_mcangle_it2
X-RAY DIFFRACTIONp_scangle_it4.5

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