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- PDB-1eeo: CRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B COMPLEXED WI... -

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Entry
Database: PDB / ID: 1eeo
TitleCRYSTAL STRUCTURE OF PROTEIN TYROSINE PHOSPHATASE 1B COMPLEXED WITH ACETYL-E-L-E-F-PTYR-M-D-Y-E-NH2
Components
  • ACETYL-E-L-E-F-PTYR-M-D-Y-E-NH2 PEPTIDE
  • PROTEIN TYROSINE PHOSPHATASE 1B
KeywordsHYDROLASE/HYDROLASE SUBSTRATE / HYDROLASE / PHOSPHORYLATION / INHIBITION / HYDROLASE-HYDROLASE SUBSTRATE 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
Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSarmiento, M. / Puius, Y.A. / Vetter, S.W. / Lawrence, D.S. / Almo, S.C. / Zhang, Z.Y.
Citation
Journal: Biochemistry / Year: 2000
Title: Structural basis of plasticity in protein tyrosine phosphatase 1B substrate recognition.
Authors: Sarmiento, M. / Puius, Y.A. / Vetter, S.W. / Keng, Y.F. / Wu, L. / Zhao, Y. / Lawrence, D.S. / Almo, S.C. / Zhang, Z.Y.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Assessment of Protein-Tyrosine Phosphatase 1B Specificity Using "Inverse Alanine Scanning"
Authors: Vetter, S.W. / Keng, Y.F. / Lawrence, D.S. / Zhang, Z.Y.
#2: Journal: J.Biol.Chem. / Year: 1998
Title: Molecular Basis of Substrate Specificity of Protein-Tyrosine Phosphatase 1B
Authors: Sarmiento, M. / Zhao, Y. / Gordon, S.J. / Zhang, Z.Y.
#3: Journal: J.Biol.Chem. / Year: 1996
Title: Determinants of Substrate Recognition in the Protein Tyrosine Phosphatase, Ptp1
Authors: Zhang, Z.Y. / Walsh, A.B. / Wu, L. / Mcnamara, D.J. / Dobrusin, E.M. / Miller, W.T.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Identification of a Second Aryl Phosphate-Binding Site in Protein-Tyrosine Phosphatase 1B: A Paradigm for Inhibitor Design
Authors: Puius, Y.A. / Zhao, Y. / Sullivan, M. / Lawrence, D.S. / Almo, S.C. / Zhang, Z.Y.
#5: Journal: Science / Year: 1995
Title: Structural Basis for Phosphotyrosine Peptide Recognition by Protein Tyrosine Phosphatase 1B
Authors: Jia, Z. / Barford, D. / Flint, A.J. / Tonks, N.K.
History
DepositionFeb 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Jul 18, 2012Group: Derived calculations
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: ACETYL-E-L-E-F-PTYR-M-D-Y-E-NH2 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7163
Polymers38,6922
Non-polymers241
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-16 kcal/mol
Surface area13940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.581, 82.050, 88.543
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 1B / PTP1B


Mass: 37349.574 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-321 / Mutation: C215S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PUC118-PTP1B-C215S / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Protein/peptide ACETYL-E-L-E-F-PTYR-M-D-Y-E-NH2 PEPTIDE


Mass: 1342.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED
#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.: 226 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2100 mMMES1drop
325 mM1dropNaCl
40.2 mMEDTA1drop
53.0 mMdithiothreitol1drop
60.150 mMpeptide1drop
70.1 MHEPES1reservoir
80.2 Mmagnesium acetate1reservoir
912-20 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 34694 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 9 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 30.3
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 14.2 / % possible all: 73.5
Reflection
*PLUS
Num. measured all: 180537
Reflection shell
*PLUS
% possible obs: 73.5 % / Num. unique obs: 2629

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AAX

1aax


Resolution: 1.8→24.09 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 493012.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1074 3.1 %RANDOM
Rwork0.183 ---
obs0.183 34624 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.23 Å2 / ksol: 0.465 e/Å3
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.55 Å20 Å20 Å2
2--6.36 Å20 Å2
3----3.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 1 226 2735
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.911.5
X-RAY DIFFRACTIONc_mcangle_it1.522
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it2.692.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.225 92 3.4 %
Rwork0.218 2579 -
obs--75 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2BPAPEP.PARBPAPEP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 3.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.225 / % reflection Rfree: 3.4 % / Rfactor Rwork: 0.218 / Rfactor obs: 0.218

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