4ZRT | pdb_00004zrt

PTP1BC215S bound to Nephrin peptide substrate

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8040614	3000304	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e4zrtA1	A: Carbon-nitrogen hydrolase-like	X: Metallo-dependent phosphatases	H: Metallo-dependent phosphatases	T: GCD14	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00102	Protein-tyrosine phosphatase (Y_phosphatase)	Protein-tyrosine phosphatase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	GLY-PRO-LEU-PTR-ASP-GLU	cell adhesion molecule binding protein binding binding cytoskeletal protein binding myosin binding	developmental process multicellular organismal process animal organ development extracellular matrix organization renal system development glomerular basement membrane development cellular component organization glomerulus development multicellular organism development anatomical structure development cellular process cellular component organization or biogenesis nephron development kidney development developmental process multicellular organismal process animal organ development extracellular matrix organization renal system development glomerular basement membrane development cellular component organization glomerulus development multicellular organism development anatomical structure development cellular process cellular component organization or biogenesis nephron development kidney development system development extracellular structure organization external encapsulating structure organization renal filtration cell differentiation kidney epithelium development cellular developmental process glomerular epithelial cell differentiation cell development epithelial cell differentiation cell differentiation nephron epithelium development epithelial cell differentiation involved in kidney development epithelium development glomerular epithelium development tissue development podocyte development epithelial cell development cell differentiation involved in kidney development glomerular epithelial cell development podocyte differentiation localization protein localization to synapse macromolecule localization intracellular protein localization protein localization to cell junction muscle structure development skeletal muscle organ development skeletal muscle tissue development muscle tissue development muscle organ development striated muscle tissue development slit diaphragm assembly filtration diaphragm assembly cellular component biogenesis cell junction organization cellular component assembly cell junction assembly cell-cell junction assembly cell-cell junction organization biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication JNK cascade intracellular signaling cassette MAPK cascade signal transduction positive regulation of organelle organization regulation of cytoskeleton organization regulation of cellular component organization regulation of actin filament-based process positive regulation of cellular component organization regulation of cellular component size positive regulation of biological process regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly positive regulation of protein polymerization protein-containing complex assembly actin filament-based process regulation of actin filament polymerization regulation of biological quality positive regulation of cellular process protein polymerization actin polymerization or depolymerization regulation of actin filament organization actin cytoskeleton organization actin filament polymerization protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of actin polymerization or depolymerization actin filament organization regulation of cellular component biogenesis positive regulation of supramolecular fiber organization regulation of organelle organization organelle organization regulation of protein polymerization regulation of actin filament length regulation of actin cytoskeleton organization regulation of supramolecular fiber organization supramolecular fiber organization positive regulation of actin filament polymerization cytoskeleton organization regulation of anatomical structure size myoblast fusion cell-cell fusion muscle cell differentiation myotube differentiation syncytium formation by plasma membrane fusion anatomical structure morphogenesis anatomical structure formation involved in morphogenesis syncytium formation striated muscle cell differentiation cell adhesion cell-cell adhesion	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell-cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell-cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle filtration diaphragm slit diaphragm cell periphery plasma membrane membrane cell projection
A	Tyrosine-protein phosphatase non-receptor type 1	phosphoric ester hydrolase activity phosphoprotein phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity protein binding binding signaling receptor binding insulin receptor binding cell adhesion molecule binding cadherin binding ephrin receptor binding phosphoric ester hydrolase activity phosphoprotein phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity protein binding binding signaling receptor binding insulin receptor binding cell adhesion molecule binding cadherin binding ephrin receptor binding protein tyrosine kinase binding kinase binding receptor tyrosine kinase binding enzyme binding protein kinase binding non-membrane spanning protein tyrosine phosphatase activity protein tyrosine phosphatase activity protein phosphatase binding phosphatase binding protein phosphatase 2A binding RNA binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus regulation of signaling regulation of biological process regulation of cellular process response to stimulus negative regulation of signaling signaling negative regulation of response to stimulus biological regulation negative regulation of biological process regulation of signal transduction negative regulation of signal transduction negative regulation of cell communication cell communication regulation of response to stimulus cellular response to stimulus regulation of signaling regulation of biological process regulation of cellular process response to stimulus negative regulation of signaling signaling negative regulation of response to stimulus biological regulation negative regulation of biological process regulation of signal transduction negative regulation of signal transduction negative regulation of cell communication cell communication regulation of response to stimulus negative regulation of cellular process regulation of cell communication cellular process signal transduction cellular response to nitrogen compound response to peptide hormone cellular response to growth hormone stimulus cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus response to hormone growth hormone receptor signaling pathway via JAK-STAT enzyme-linked receptor protein signaling pathway cellular response to hormone stimulus growth hormone receptor signaling pathway cell surface receptor signaling pathway response to endogenous stimulus cellular response to peptide hormone stimulus response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound response to growth hormone cellular response to chemical stimulus response to chemical heart process multicellular organismal process system process regulation of heart contraction regulation of system process positive regulation of biological process positive regulation of heart rate positive regulation of blood circulation positive regulation of heart contraction circulatory system process regulation of blood circulation positive regulation of multicellular organismal process regulation of multicellular organismal process regulation of biological quality heart contraction blood circulation regulation of heart rate regulation of catalytic activity negative regulation of catalytic activity regulation of transferase activity regulation of MAP kinase activity intracellular signal transduction regulation of primary metabolic process negative regulation of kinase activity phosphate-containing compound metabolic process intracellular signaling cassette negative regulation of protein modification process phosphorus metabolic process protein modification process negative regulation of protein metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of MAPK cascade regulation of molecular function regulation of kinase activity negative regulation of protein phosphorylation regulation of protein serine/threonine kinase activity macromolecule modification regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein modification process regulation of protein phosphorylation negative regulation of intracellular signal transduction negative regulation of phosphate metabolic process regulation of intracellular signal transduction negative regulation of protein serine/threonine kinase activity protein metabolic process negative regulation of macromolecule metabolic process negative regulation of molecular function negative regulation of MAP kinase activity regulation of protein kinase activity regulation of macromolecule metabolic process negative regulation of protein kinase activity negative regulation of phosphorus metabolic process MAPK cascade regulation of phosphorylation negative regulation of phosphorylation negative regulation of MAPK cascade regulation of localization import into cell regulation of cellular component organization regulation of transport transport regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport cellular component organization localization cellular component organization or biogenesis endocytosis regulation of endocytosis response to decreased oxygen levels cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to stress response to hypoxia response to stress response to oxygen levels response to abiotic stimulus platelet-derived growth factor receptor-beta signaling pathway platelet-derived growth factor receptor signaling pathway regulation of proteolysis proteolysis negative regulation of ERK1 and ERK2 cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade cellular response to growth factor stimulus negative regulation of cellular response to growth factor stimulus regulation of vascular endothelial growth factor receptor signaling pathway negative regulation of vascular endothelial growth factor receptor signaling pathway regulation of cellular response to growth factor stimulus vascular endothelial growth factor receptor signaling pathway response to growth factor organelle organization actin cytoskeleton organization actin filament-based process cytoskeleton organization regulation of neuron projection development cellular developmental process cell projection organization cell development neuron projection development neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cell projection organization system development developmental process plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization nervous system development negative regulation of neuron projection development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization response to fibroblast growth factor cellular response to fibroblast growth factor stimulus cellular response to nerve growth factor stimulus response to nerve growth factor establishment of protein localization cellular localization regulation of protein localization establishment of localization in cell intracellular protein localization regulation of intracellular transport regulation of establishment of protein localization intracellular transport regulation of protein transport protein transport regulation of cellular localization macromolecule localization regulation of intracellular protein transport intracellular protein transport receptor catabolic process catabolic process regulation of catabolic process macromolecule catabolic process positive regulation of catabolic process positive regulation of metabolic process receptor metabolic process regulation of receptor catabolic process positive regulation of macromolecule metabolic process positive regulation of receptor catabolic process positive regulation of cellular process insulin receptor signaling pathway regulation of cellular response to insulin stimulus regulation of insulin receptor signaling pathway negative regulation of cellular response to insulin stimulus negative regulation of insulin receptor signaling pathway response to insulin cellular response to insulin stimulus positive regulation of IRE1-mediated unfolded protein response positive regulation of cell communication positive regulation of signal transduction regulation of cellular response to stress endoplasmic reticulum unfolded protein response regulation of response to endoplasmic reticulum stress positive regulation of response to stimulus regulation of endoplasmic reticulum unfolded protein response positive regulation of response to endoplasmic reticulum stress regulation of response to stress positive regulation of endoplasmic reticulum unfolded protein response response to endoplasmic reticulum stress regulation of IRE1-mediated unfolded protein response cellular response to topologically incorrect protein positive regulation of intracellular signal transduction cellular response to unfolded protein response to unfolded protein response to topologically incorrect protein IRE1-mediated unfolded protein response positive regulation of signaling positive regulation of JNK cascade JNK cascade positive regulation of MAPK cascade regulation of JNK cascade regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction cellular response to oscillatory fluid shear stress response to oscillatory fluid shear stress response to fluid shear stress vascular endothelial cell response to oscillatory fluid shear stress vascular endothelial cell response to fluid shear stress cellular response to fluid shear stress regulation of hepatocyte growth factor receptor signaling pathway hepatocyte growth factor receptor signaling pathway response to nutrient levels positive regulation of systemic arterial blood pressure regulation of systemic arterial blood pressure regulation of blood pressure positive regulation of blood pressure cellular response to nitric oxide response to nitric oxide cellular response to reactive nitrogen species cellular response to platelet-derived growth factor stimulus response to platelet-derived growth factor positive regulation of cellular response to insulin stimulus positive regulation of insulin receptor signaling pathway receptor recycling insulin receptor recycling negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway regulation of programmed cell death intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress regulation of intrinsic apoptotic signaling pathway regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway intrinsic apoptotic signaling pathway negative regulation of response to endoplasmic reticulum stress negative regulation of programmed cell death regulation of apoptotic process cell death apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway negative regulation of apoptotic process apoptotic process programmed cell death regulation of apoptotic signaling pathway regulation of vascular associated smooth muscle cell migration negative regulation of locomotion vascular associated smooth muscle cell migration regulation of cell motility negative regulation of vascular associated smooth muscle cell migration regulation of smooth muscle cell migration smooth muscle cell migration muscle cell migration negative regulation of smooth muscle cell migration regulation of locomotion regulation of cell migration negative regulation of cell motility cell migration cell motility locomotion negative regulation of cell migration positive regulation of cardiac muscle cell apoptotic process positive regulation of programmed cell death muscle cell apoptotic process positive regulation of striated muscle cell apoptotic process regulation of cardiac muscle cell apoptotic process regulation of muscle cell apoptotic process positive regulation of apoptotic process cardiac muscle cell apoptotic process positive regulation of muscle cell apoptotic process regulation of striated muscle cell apoptotic process striated muscle cell apoptotic process cellular component biogenesis cellular component assembly regulation of postsynapse assembly cell junction assembly regulation of synapse structure or activity synapse organization regulation of synapse assembly postsynapse organization postsynapse assembly regulation of postsynapse organization regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation regulation of cell-substrate adhesion regulation of cell adhesion cell-substrate adhesion negative regulation of cell adhesion cell adhesion negative regulation of cell-substrate adhesion protein dephosphorylation dephosphorylation peptidyl-tyrosine dephosphorylation positive regulation of endothelial cell apoptotic process endothelial cell apoptotic process regulation of endothelial cell apoptotic process regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus regulation of type I interferon-mediated signaling pathway response to cytokine response to biotic stimulus cytokine-mediated signaling pathway interferon-mediated signaling pathway cellular response to type I interferon innate immune response regulation of immune system process cellular response to cytokine stimulus response to external biotic stimulus immune response response to other organism defense response regulation of innate immune response regulation of cytokine-mediated signaling pathway defense response to symbiont response to external stimulus response to peptide regulation of response to cytokine stimulus immune system process defense response to other organism type I interferon-mediated signaling pathway regulation of immune response response to type I interferon PERK-mediated unfolded protein response integrated stress response signaling ER-nucleus signaling pathway negative regulation of endoplasmic reticulum unfolded protein response regulation of PERK-mediated unfolded protein response negative regulation of PERK-mediated unfolded protein response response to angiotensin cellular response to angiotensin	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse membrane-bounded organelle organelle subcompartment cytoplasmic side of membrane membrane intracellular membrane-bounded organelle endomembrane system side of membrane cellular anatomical structure intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse membrane-bounded organelle organelle subcompartment cytoplasmic side of membrane membrane intracellular membrane-bounded organelle endomembrane system side of membrane endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasmic side of endoplasmic reticulum membrane organelle membrane endoplasmic reticulum membrane sorting endosome endosome intracellular vesicle cytoplasmic vesicle vesicle postsynapse mitochondrial membrane organelle inner membrane mitochondrion mitochondrial inner membrane organelle envelope mitochondrial envelope mitochondrial crista protein-containing complex early endosome membrane-enclosed lumen intracellular organelle lumen organelle lumen endosome lumen mitochondrial matrix

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B	IPR003598	Immunoglobulin subtype 2	Domain
B	IPR013106	Immunoglobulin V-set domain	Domain
B	IPR003599	Immunoglobulin domain subtype	Domain
B	IPR013098	Immunoglobulin I-set	Domain
B	IPR051275	Cellular adhesion and signaling domain-containing protein	Family
B	IPR003961	Fibronectin type III	Domain
B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B	IPR013162	CD80-like, immunoglobulin C2-set	Domain
B	IPR007110	Immunoglobulin-like domain	Domain
B	IPR036116	Fibronectin type III superfamily	Homologous Superfamily
A	IPR016130	Protein-tyrosine phosphatase, active site	Active Site
A	IPR051985	Non-receptor type tyrosine-specific phosphatase	Family
A	IPR012265	Protein-tyrosine phosphatase, non-receptor type-1/2	Family
A	IPR003595	Protein-tyrosine phosphatase, catalytic	Domain
A	IPR029021	Protein-tyrosine phosphatase-like	Homologous Superfamily
A	IPR000242	Tyrosine-specific protein phosphatase, PTPase domain	Domain
A	IPR000387	Tyrosine-specific protein phosphatases domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: O60500	familial nephrotic syndrome proteinuria glomerulonephritis lipoid nephrosis Albuminuria hyperhomocysteinemia kidney disease nephrotic syndrome congenital nephrotic syndrome, Finnish type focal segmental glomerulosclerosis nephritis idiopathic nephrotic syndrome kidney failure nephrotic syndrome, type 3 intellectual disability
A	Pharos: P18031	type 2 diabetes mellitus Insulin Resistance Rett syndrome obesity disorder hypertensive disorder hyperinsulinism B-cell neoplasm Hodgkins lymphoma lung cancer maturity-onset diabetes of the young colorectal adenoma ovarian cancer schizophrenia Hodgkin's lymphoma, mixed cellularity Huntington disease type 2 diabetes mellitus Insulin Resistance Rett syndrome obesity disorder hypertensive disorder hyperinsulinism B-cell neoplasm Hodgkins lymphoma lung cancer maturity-onset diabetes of the young colorectal adenoma ovarian cancer schizophrenia Hodgkin's lymphoma, mixed cellularity Huntington disease inborn carbohydrate metabolic disorder mediastinal cancer nodular lymphocyte predominant Hodgkin lymphoma colorectal cancer Hodgkin's lymphoma, lymphocytic depletion sarcoidosis vitiligo Hodgkin's lymphoma, lymphocytic-histiocytic predominance

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	PTR	Parent Component: TYR RESID: AA0039 PSI-MOD : O4'-phospho-L-tyrosine MOD:00048

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.