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- PDB-6b95: Multiconformer model of K197C PTP1B tethered to compound 2 at 100 K -

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Basic information

Entry
Database: PDB / ID: 6b95
TitleMulticonformer model of K197C PTP1B tethered to compound 2 at 100 K
ComponentsTyrosine-protein phosphatase non-receptor type 1
KeywordsSIGNALING PROTEIN / protein tyrosine phosphatase / PTP / protein tyrosine phosphatase 1B / PTP1B / enzyme / allostery / multitemperature / multiconformer / tethering / covalent ligand
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 / IRE1-mediated unfolded protein response / positive regulation of protein tyrosine kinase activity / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome ...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 / IRE1-mediated unfolded protein response / positive regulation of protein tyrosine kinase activity / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / negative regulation of vascular associated smooth muscle cell migration / mitochondrial crista / cytoplasmic side of endoplasmic reticulum membrane / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / negative regulation of PERK-mediated unfolded protein response / positive regulation of JUN kinase activity / positive regulation of systemic arterial blood pressure / negative regulation of MAP kinase activity / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / peptidyl-tyrosine dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / Regulation of IFNA/IFNB signaling / regulation of proteolysis / cellular response to angiotensin / regulation of postsynapse assembly / positive regulation of endothelial cell apoptotic process / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of cell-substrate adhesion / cellular response to unfolded protein / regulation of signal transduction / Regulation of IFNG signaling / negative regulation of signal transduction / Growth hormone receptor signaling / positive regulation of heart rate / positive regulation of cardiac muscle cell apoptotic process / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein dephosphorylation / endoplasmic reticulum unfolded protein response / MECP2 regulates neuronal receptors and channels / ephrin receptor binding / Insulin receptor recycling / cellular response to platelet-derived growth factor stimulus / cellular response to fibroblast growth factor stimulus / Integrin signaling / protein-tyrosine-phosphatase / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to nitric oxide / negative regulation of insulin receptor signaling pathway / protein tyrosine phosphatase activity / protein phosphatase 2A binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / endosome lumen / insulin receptor binding / response to nutrient levels / Negative regulation of MET activity / cellular response to nerve growth factor stimulus / receptor tyrosine kinase binding / negative regulation of ERK1 and ERK2 cascade / insulin receptor signaling pathway / negative regulation of neuron projection development / actin cytoskeleton organization / cellular response to hypoxia / early endosome / postsynapse / cadherin binding / mitochondrial matrix / negative regulation of cell population proliferation / protein kinase binding / glutamatergic synapse / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytoplasm / cytosol
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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-D0P / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsKeedy, D.A. / Hill, Z.B. / Biel, J.T. / Kang, E. / Rettenmaier, T.J. / Brandao-Neto, J. / von Delft, F. / Wells, J.A. / Fraser, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Elife / Year: 2018
Title: An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.
Authors: Keedy, D.A. / Hill, Z.B. / Biel, J.T. / Kang, E. / Rettenmaier, T.J. / Brandao-Neto, J. / Pearce, N.M. / von Delft, F. / Wells, J.A. / Fraser, J.S.
History
DepositionOct 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Tyrosine-protein phosphatase non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7373
Polymers37,3201
Non-polymers4172
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint4 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.960, 87.960, 104.630
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 37319.527 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: C32S, C92V, K197C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-D0P / N-(2',4'-difluoro-4-hydroxy[1,1'-biphenyl]-3-yl)-2-sulfanylacetamide


Mass: 295.304 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11F2NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: well solution: 0.2 M magnesium acetate tetrahydrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.95→43.98 Å / Num. obs: 34580 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.917 % / Biso Wilson estimate: 38.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.098 / Χ2: 1.013 / Net I/σ(I): 11.61 / Num. measured all: 170040 / Scaling rejects: 79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.95-24.9931.8370.8112558251625150.2812.053100
2-2.064.8811.6590.9512037247124660.3691.85999.8
2.06-2.124.6651.1671.2911127238723850.4671.31599.9
2.12-2.184.7710.8481.8111135233523340.6380.953100
2.18-2.255.1570.6842.3911752228022790.7590.761100
2.25-2.335.1230.5792.8911045215821560.8030.64499.9
2.33-2.425.0980.4283.8510834212621250.8860.477100
2.42-2.525.0590.3454.6910305203920370.9120.38599.9
2.52-2.634.8960.2646.149610196419630.9560.29599.9
2.63-2.764.6090.1997.48669188418810.9710.22599.8
2.76-2.915.1480.15710.289195178617860.9830.175100
2.91-3.085.1790.10814.018732168616860.9930.121100
3.08-3.35.1120.08218.488133159215910.9950.09199.9
3.3-3.564.9990.05425.337473149614950.9980.06199.9
3.56-3.94.4260.04729.256046137513660.9980.05399.3
3.9-4.364.8250.03537.186084126512610.9990.03999.7
4.36-5.034.820.03142.545288111410970.9990.03598.5
5.03-6.174.8250.03339.3846229609580.9990.03799.8
6.17-8.724.3650.02940.5432917587540.9990.03399.5
8.72-43.984.7280.02152.321044484450.9990.02499.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSJun 1, 2017data reduction
XSCALEJun 1, 2017data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→43.98 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2307 1362 3.94 %
Rwork0.1858 33208 -
obs0.1875 34570 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.79 Å2 / Biso mean: 54.6943 Å2 / Biso min: 21 Å2
Refinement stepCycle: final / Resolution: 1.95→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 70 135 2525
Biso mean--57.73 52 -
Num. residues----285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122465
X-RAY DIFFRACTIONf_angle_d1.1583332
X-RAY DIFFRACTIONf_chiral_restr0.06349
X-RAY DIFFRACTIONf_plane_restr0.008432
X-RAY DIFFRACTIONf_dihedral_angle_d14.2621498
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9501-2.01980.36871350.329632513386100
2.0198-2.10060.33291350.297833063441100
2.1006-2.19620.26611330.25932763409100
2.1962-2.3120.30381350.228732923427100
2.312-2.45680.2811380.202632903428100
2.4568-2.64650.21761390.186832883427100
2.6465-2.91280.23111370.184133253462100
2.9128-3.33420.21661350.170733423477100
3.3342-4.20020.21621350.14633573492100
4.2002-43.99120.20351400.18033481362199

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