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- PDB-4j51: Cyrstal structure of protein tyrosine phosphatase Lyp catalytic d... -

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Basic information

Entry
Database: PDB / ID: 4j51
TitleCyrstal structure of protein tyrosine phosphatase Lyp catalytic domain complex with small molecular inhibitor L75N04
ComponentsTyrosine-protein phosphatase non-receptor type 22
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / TYROSINE PHOSPHATASE / inhibitor design / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


phosphoanandamide dephosphorylation / positive regulation of granzyme B production / positive regulation of toll-like receptor 3 signaling pathway / regulation of natural killer cell proliferation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of toll-like receptor 9 signaling pathway ...phosphoanandamide dephosphorylation / positive regulation of granzyme B production / positive regulation of toll-like receptor 3 signaling pathway / regulation of natural killer cell proliferation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of toll-like receptor 9 signaling pathway / regulation of non-canonical NF-kappaB signal transduction / negative regulation of T cell activation / positive regulation of protein K63-linked ubiquitination / cellular response to muramyl dipeptide / negative regulation of interleukin-8 production / negative regulation of JUN kinase activity / negative regulation of T cell receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of CD8-positive, alpha-beta T cell proliferation / regulation of innate immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / phosphatase activity / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / non-membrane spanning protein tyrosine phosphatase activity / T cell differentiation / positive regulation of type I interferon production / lipopolysaccharide-mediated signaling pathway / positive regulation of defense response to virus by host / negative regulation of autophagy / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / lipid metabolic process / cytoplasmic side of plasma membrane / autophagy / kinase binding / SH3 domain binding / positive regulation of type II interferon production / T cell receptor signaling pathway / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / negative regulation of gene expression / ubiquitin protein ligase binding / positive regulation of gene expression / perinuclear region of cytoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Non-receptor tyrosine-protein phosphatase 22 / : / 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 ...: / Non-receptor tyrosine-protein phosphatase 22 / : / 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-N75 / Tyrosine-protein phosphatase non-receptor type 22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLiu, D. / He, Y. / Zhang, Z.-Y.
CitationJournal: J.Med.Chem. / Year: 2013
Title: A Potent and Selective Small-Molecule Inhibitor for the Lymphoid-Specific Tyrosine Phosphatase (LYP), a Target Associated with Autoimmune Diseases.
Authors: He, Y. / Liu, S. / Menon, A. / Stanford, S. / Oppong, E. / Gunawan, A.M. / Wu, L. / Wu, D.J. / Barrios, A.M. / Bottini, N. / Cato, A.C. / Zhang, Z.Y.
History
DepositionFeb 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 22
B: Tyrosine-protein phosphatase non-receptor type 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2694
Polymers76,2652
Non-polymers1,0042
Water86548
1
A: Tyrosine-protein phosphatase non-receptor type 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6352
Polymers38,1331
Non-polymers5021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6352
Polymers38,1331
Non-polymers5021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.193, 93.644, 153.498
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 Tyrosine-protein phosphatase non-receptor type 22 / Hematopoietic cell protein-tyrosine phosphatase 70Z-PEP / Lymphoid phosphatase / LyP / PEST-domain ...Hematopoietic cell protein-tyrosine phosphatase 70Z-PEP / Lymphoid phosphatase / LyP / PEST-domain phosphatase / PEP


Mass: 38132.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN22, PTPN8 / Plasmid: pETDE3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2R2, protein-tyrosine-phosphatase
#2: Chemical ChemComp-N75 / 3-[(3-chlorophenyl)ethynyl]-2-{4-[2-(cyclopropylamino)-2-oxoethoxy]phenyl}-6-hydroxy-1-benzofuran-5-carboxylic acid


Mass: 501.915 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H20ClNO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.2 M sodium formate (pH 7.2) and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 28140 / % possible obs: 93.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.065

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.1refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry code 2P6X

2p6x


Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 1284 -random
Rwork0.1887 ---
obs-26388 86.7 %-
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4996 0 72 48 5116
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0097
X-RAY DIFFRACTIONc_angle_deg1.42

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