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- PDB-1bzh: Cyclic peptide inhibitor of human PTP1B -

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Basic information

Entry
Database: PDB / ID: 1bzh
TitleCyclic peptide inhibitor of human PTP1B
Components
  • PROTEIN (PROTEIN-TYROSINE-PHOSPHATASE 1B INHIBITOR)
  • PROTEIN (PROTEIN-TYROSINE-PHOSPHATASE 1B)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PHOSPHORYLATION-INHIBITOR COMPLEX / TYROSINE PHOSPHATASE / 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 / 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
Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGroves, M.R. / Yao, Z.J. / Burke Jr., T.R. / Barford, D.
Citation
Journal: Biochemistry / Year: 1998
Title: Structural basis for inhibition of the protein tyrosine phosphatase 1B by phosphotyrosine peptide mimetics.
Authors: Groves, M.R. / Yao, Z.J. / Roller, P.P. / Burke Jr., T.R. / Barford, D.
#1: Journal: Science / Year: 1994
Title: Crystal Structure of Human Protein Tyrosine Phosphatase 1B
Authors: Barford, D. / Flint, A.J. / Tonks, N.K.
History
DepositionOct 28, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 16, 1999Provider: 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 2.0Dec 26, 2018Group: Data collection / Polymer sequence / Category: chem_comp / entity_poly
Item: _chem_comp.mon_nstd_flag / _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Aug 9, 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_conn / struct_ref_seq_dif
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
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PROTEIN-TYROSINE-PHOSPHATASE 1B)
I: PROTEIN (PROTEIN-TYROSINE-PHOSPHATASE 1B INHIBITOR)


Theoretical massNumber of molelcules
Total (without water)35,7262
Polymers35,7262
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.690, 86.820, 52.000
Angle α, β, γ (deg.)90.00, 96.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (PROTEIN-TYROSINE-PHOSPHATASE 1B) / PTP1B


Mass: 34720.566 Da / Num. of mol.: 1 / 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: Protein/peptide PROTEIN (PROTEIN-TYROSINE-PHOSPHATASE 1B INHIBITOR)


Mass: 1004.944 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.72 Å3/Da / Density % sol: 54.47 %
Crystal growpH: 8 / Details: pH 8.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 %(w/v)PEG40001reservoir
20.2 M1reservoirMgCl2
30.1 MHEPES1reservoir
410 mg/mlprotein1drop
55 mMFOMT1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→8 Å / Num. obs: 15934 / % possible obs: 78.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.029 / Rsym value: 0.029 / Net I/σ(I): 13.7
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 8.8 / Rsym value: 0.074 / % possible all: 55.7
Reflection
*PLUS
Num. measured all: 46108
Reflection shell
*PLUS
% possible obs: 55.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HNP

2hnp


Resolution: 2.1→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 997 6.67 %THIN SHELLS
Rwork0.196 ---
obs-15934 78.1 %-
Displacement parametersBiso mean: 65.49 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 0 0 88 2583
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4082
X-RAY DIFFRACTIONp_mcangle_it2.2693
X-RAY DIFFRACTIONp_scbond_it1.4452
X-RAY DIFFRACTIONp_scangle_it2.3193
X-RAY DIFFRACTIONp_plane_restr0.01960.03
X-RAY DIFFRACTIONp_chiral_restr0.1110.15
X-RAY DIFFRACTIONp_singtor_nbd0.1880.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1860.3
X-RAY DIFFRACTIONp_planar_tor3.37
X-RAY DIFFRACTIONp_staggered_tor17.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.420
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / σ(F): 0 / % reflection Rfree: 6.67 % / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_plane_restr / Dev ideal target: 0.03
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.21 Å / Rfactor Rfree: 0.336 / Rfactor obs: 0.31

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