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- PDB-1lqf: Structure of PTP1b in Complex with a Peptidic Bisphosphonate Inhibitor -

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Basic information

Entry
Database: PDB / ID: 1lqf
TitleStructure of PTP1b in Complex with a Peptidic Bisphosphonate Inhibitor
Componentsprotein-tyrosine phosphatase, non-receptor type 1
KeywordsHYDROLASE / Phosphatase / phosphonates / diabetes / inhibitor
Function / homology
Function and homology information


regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / positive regulation of receptor catabolic process / insulin receptor recycling / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of PERK-mediated unfolded protein response / 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 / positive regulation of receptor catabolic process / insulin receptor recycling / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of PERK-mediated unfolded protein response / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / mitochondrial crista / 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 / positive regulation of protein tyrosine kinase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / 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 / Growth hormone receptor signaling / endoplasmic reticulum unfolded protein response / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / ephrin receptor binding / Integrin signaling / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of MAP kinase activity / 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 ...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-BGD / Tyrosine-protein phosphatase non-receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAsante-Appiah, E. / Patel, S. / Dufresne, C. / Scapin, G.
Citation
Journal: Biochemistry / Year: 2002
Title: The structure of PTP-1B in complex with a peptide inhibitor reveals an alternative binding mode for bisphosphonates.
Authors: Asante-Appiah, E. / Patel, S. / Dufresne, C. / Roy, P. / Wang, Q. / Patel, V. / Friesen, R.W. / Ramachandran, C. / Becker, J.W. / Leblanc, Y. / Kennedy, B.P. / Scapin, G.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: The YRD motif is a major determinant of substrate and inhibitor specificity in T-cell protein-tyrosine phosphatase
Authors: Asante-Appiah, E. / Ball, K. / Bateman, K. / Skorey, K. / Friesen, R. / Desponts, C. / Payette, P. / Bayly, C. / Zamboni, R. / Scapin, G. / Ramachandran, C. / Kennedy, B.P.
History
DepositionMay 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 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, non-receptor type 1
B: protein-tyrosine phosphatase, non-receptor type 1
C: protein-tyrosine phosphatase, non-receptor type 1
D: protein-tyrosine phosphatase, non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,0248
Polymers137,8054
Non-polymers3,2184
Water9,512528
1
A: protein-tyrosine phosphatase, non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2562
Polymers34,4511
Non-polymers8051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: protein-tyrosine phosphatase, non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2562
Polymers34,4511
Non-polymers8051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: protein-tyrosine phosphatase, non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2562
Polymers34,4511
Non-polymers8051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: protein-tyrosine phosphatase, non-receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2562
Polymers34,4511
Non-polymers8051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.866, 154.421, 64.598
Angle α, β, γ (deg.)90.00, 94.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-3371-

HOH

21B-3426-

HOH

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Components

#1: Protein
protein-tyrosine phosphatase, non-receptor type 1 / PTP1B / Protein Tyrosine Phosphatase 1B


Mass: 34451.367 Da / Num. of mol.: 4 / Fragment: catalytic domain (residues 1-283)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-BGD / N-BENZOYL-L-GLUTAMYL-[4-PHOSPHONO(DIFLUOROMETHYL)]-L-PHENYLALANINE-[4-PHOSPHONO(DIFLUORO-METHYL)]-L-PHENYLALANINEAMIDE / 4-BENZOYLAMINO-4-{1-{1-CARBAMOYL-2-[4-(DIFLUORO-PHOSPHONO-METHYL)-PHENYL]-ETHYLCARBAMOYL}-2-[4-(DIFLUORO-PHOSPHONO-METHYL)-PHENYL]-ETHYLCARBAMOYL}-BUTYRIC ACID


Mass: 804.573 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H34F4N4O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 3.7 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 284 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: Peg 4000, propanol, citrate, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 284K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
220 mMHEPES1droppH7.0
350 mM1dropNaCl
41 mMEDTA1drop
52 mMDMH1drop
614 %PEG40001reservoir
710 %propanol1reservoir
8100 mMcitrate1reservoirpH5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 9, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→29 Å / Num. all: 63052 / Num. obs: 61097 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 38.9 Å2 / Rsym value: 0.121 / Net I/σ(I): 6
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 9039 / Rsym value: 0.38 / % possible all: 86.4
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 176274 / Rmerge(I) obs: 0.121
Reflection shell
*PLUS
% possible obs: 86.4 % / Num. unique obs: 9039 / Num. measured obs: 17193 / Rmerge(I) obs: 0.38

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
MAR345data collection
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PTY

1pty


Resolution: 2.5→29 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: A 4% twinning was detected using both Truncate and CNS and the refinement was carried out using the CNS twinning procedures, with twinning operator h, -k, -l.
RfactorNum. reflection% reflectionSelection details
Rfree0.286 2769 -Random
Rwork0.228 ---
obs0.231 54787 91.4 %-
all-59942 --
Displacement parametersBiso mean: 42.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.15 Å20 Å2-1.747 Å2
2---6.688 Å20 Å2
3---1.537 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9332 0 216 528 10076
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.52
X-RAY DIFFRACTIONc_dihedral_angle_d23.02
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shellResolution: 2.5→2.68 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.438 192 4 %
Rwork0.366 3920 -
obs--49 %
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 61052 / % reflection Rfree: 5 % / Rfactor obs: 0.231 / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.02
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
LS refinement shell
*PLUS
Rfactor Rfree: 0.438 / Rfactor Rwork: 0.366

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