[English] 日本語
Yorodumi
- PDB-1bzc: HUMAN PTP1B CATALYTIC DOMAIN COMPLEXED WITH TPI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bzc
TitleHUMAN PTP1B CATALYTIC DOMAIN COMPLEXED WITH TPI
ComponentsPROTEIN (PROTEIN-TYROSINE-PHOSPHATASE)
KeywordsHYDROLASE / HYDROLASE(PHOSPHORYLATION) / TYROSINE PHOSPHATASE / 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 / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / positive regulation of protein tyrosine kinase activity / IRE1-mediated unfolded protein response / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway ...PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / positive regulation of protein tyrosine kinase activity / IRE1-mediated unfolded protein response / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / cytoplasmic side of endoplasmic reticulum membrane / negative regulation of vascular associated smooth muscle cell migration / positive regulation of IRE1-mediated unfolded protein response / positive regulation of systemic arterial blood pressure / regulation of type I interferon-mediated signaling pathway / negative regulation of PERK-mediated unfolded protein response / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / Regulation of IFNA/IFNB signaling / peptidyl-tyrosine dephosphorylation / regulation of postsynapse assembly / regulation of proteolysis / positive regulation of JUN kinase activity / cellular response to fibroblast growth factor stimulus / growth hormone receptor signaling pathway via JAK-STAT / cellular response to angiotensin / positive regulation of endothelial cell apoptotic process / negative regulation of cell-substrate adhesion / negative regulation of MAP kinase activity / cellular response to unfolded protein / regulation of signal transduction / negative regulation of signal transduction / Regulation of IFNG signaling / Growth hormone receptor signaling / positive regulation of heart rate / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / positive regulation of cardiac muscle cell apoptotic process / protein dephosphorylation / MECP2 regulates neuronal receptors and channels / Insulin receptor recycling / cellular response to platelet-derived growth factor stimulus / ephrin receptor binding / protein tyrosine phosphatase activity / Integrin signaling / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of insulin receptor signaling pathway / cellular response to nitric oxide / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein phosphatase 2A binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / endosome lumen / insulin receptor binding / cellular response to nerve growth factor stimulus / response to nutrient levels / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MET activity / receptor tyrosine kinase binding / insulin receptor signaling pathway / negative regulation of neuron projection development / actin cytoskeleton organization / cellular response to hypoxia / early endosome / postsynapse / mitochondrial matrix / cadherin binding / negative regulation of cell population proliferation / protein kinase binding / glutamatergic synapse / 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-TPI / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGroves, M.R. / Yao, Z.J. / Jr Burke, 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: The Crystal Structure of Human Protein Tyrosine Phosphatase 1B
Authors: Barford, D. / Flint, A.J. / Tonks, N.K.
History
DepositionOct 27, 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: Version format compliance
Revision 1.3Aug 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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (PROTEIN-TYROSINE-PHOSPHATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7962
Polymers37,3661
Non-polymers4301
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.470, 88.470, 104.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein PROTEIN (PROTEIN-TYROSINE-PHOSPHATASE)


Mass: 37365.637 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical ChemComp-TPI / 4-CARBAMOYL-4-{[6-(DIFLUORO-PHOSPHONO-METHYL)-NAPHTHALENE-2-CARBONYL]-AMINO}-BUTYRIC ACID


Mass: 430.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17F2N2O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.62 %
Crystal growpH: 8 / Details: pH 8.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion / Details: Barfoed, D., (1994) J. Mol. Biol., 239, 726.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 MHEPES1reservoir
30.2 Mmagnesium acetate1reservoir
412-16 %(w/v)PEG80001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→24 Å / Num. obs: 28772 / % possible obs: 94.4 % / Redundancy: 2.3 % / Biso Wilson estimate: 33.99 Å2 / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 16.8
Reflection shellResolution: 2.35→2.48 Å / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 8.2 / Rsym value: 0.089 / % possible all: 93.8
Reflection
*PLUS
Num. obs: 18772 / Num. measured all: 65906
Reflection shell
*PLUS
% possible obs: 93.8 %

-
Processing

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

2hnp


Resolution: 2.35→14 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: VALUES QUOTED FOR PLANAR RESTRAINTS ARE FOR THE AROMATICS. PEPTIDE VALUES ARE RMS=0.0132, SIGMA=0.03.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 954 5 %THIN SHELLS
Rwork0.204 ---
obs-18772 94.4 %-
Displacement parametersBiso mean: 25.98 Å2
Refinement stepCycle: LAST / Resolution: 2.35→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 29 157 2612
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.0240.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0250.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.05
X-RAY DIFFRACTIONp_mcbond_it2.5822
X-RAY DIFFRACTIONp_mcangle_it4.0393
X-RAY DIFFRACTIONp_scbond_it3.8652
X-RAY DIFFRACTIONp_scangle_it5.5653
X-RAY DIFFRACTIONp_plane_restr0.01640.02
X-RAY DIFFRACTIONp_chiral_restr0.1150.15
X-RAY DIFFRACTIONp_singtor_nbd00.3
X-RAY DIFFRACTIONp_multtor_nbd0.1730.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1020.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1020.3
X-RAY DIFFRACTIONp_planar_tor1.47
X-RAY DIFFRACTIONp_staggered_tor14.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor33.820
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_plane_restr0.02
X-RAY DIFFRACTIONp_mcbond_it2
X-RAY DIFFRACTIONp_scbond_it2
X-RAY DIFFRACTIONp_mcangle_it3
X-RAY DIFFRACTIONp_scangle_it3
LS refinement shell
*PLUS
Highest resolution: 2.35 Å / Lowest resolution: 2.48 Å / Rfactor Rfree: 0.278 / Rfactor obs: 0.253

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more