3OMH | pdb_00003omh

Crystal structure of PTPN22 in complex with SKAP-HOM pTyr75 peptide

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)
D	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8078061	3000304	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8078061	3000304	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8078061	3000304	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8078061	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)
D	Y_phosphatase	e3omhD1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: (Phosphotyrosine protein) phosphatases II	F: Y_phosphatase	ECOD (1.6)
C	Y_phosphatase	e3omhC1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: (Phosphotyrosine protein) phosphatases II	F: Y_phosphatase	ECOD (1.6)
B	Y_phosphatase	e3omhB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: (Phosphotyrosine protein) phosphatases II	F: Y_phosphatase	ECOD (1.6)
A	Y_phosphatase	e3omhA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: (Phosphotyrosine protein) phosphatases II	F: Y_phosphatase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (4.3.0)
C	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (4.3.0)
B	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (4.3.0)
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, B, C, D	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
E, F, G, H	Src kinase-associated phosphoprotein 2	-	multicellular organismal process immune system process B cell activation cell activation cellular process lymphocyte activation leukocyte activation negative regulation of cell population proliferation regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation negative regulation of cellular process biological regulation multicellular organismal process immune system process B cell activation cell activation cellular process lymphocyte activation leukocyte activation negative regulation of cell population proliferation regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation negative regulation of cellular process biological regulation negative regulation of biological process cellular response to stimulus response to stimulus signaling signal transduction cell communication	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
A, B, C, D	Tyrosine-protein phosphatase non-receptor type 22	phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity SH3 domain binding protein binding binding protein domain specific binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding phosphoprotein phosphatase activity non-membrane spanning protein tyrosine phosphatase activity phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity SH3 domain binding protein binding binding protein domain specific binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding phosphoprotein phosphatase activity non-membrane spanning protein tyrosine phosphatase activity catalytic activity, acting on a protein protein tyrosine phosphatase activity kinase binding	multicellular organismal process regulation of tumor necrosis factor production regulation of cellular process negative regulation of biological process negative regulation of tumor necrosis factor production cytokine production regulation of cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation multicellular organismal process regulation of tumor necrosis factor production regulation of cellular process negative regulation of biological process negative regulation of tumor necrosis factor production cytokine production regulation of cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation tumor necrosis factor superfamily cytokine production negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process tumor necrosis factor production regulation of gene expression negative regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of tumor necrosis factor superfamily cytokine production metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process interleukin-6 production regulation of interleukin-6 production negative regulation of interleukin-6 production positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of gene expression positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process catabolic process autophagy process utilizing autophagic mechanism positive regulation of cell communication cellular response to stimulus positive regulation of response to biotic stimulus positive regulation of signal transduction response to stimulus pattern recognition receptor signaling pathway regulation of signal transduction response to biotic stimulus intracellular signal transduction cell communication immune response-activating signaling pathway positive regulation of toll-like receptor 3 signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process innate immune response-activating signaling pathway positive regulation of pattern recognition receptor signaling pathway immune response response to other organism regulation of innate immune response response to external stimulus positive regulation of intracellular signal transduction regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway positive regulation of defense response regulation of immune response activation of innate immune response activation of immune response regulation of defense response cytoplasmic pattern recognition receptor signaling pathway regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus intracellular receptor signaling pathway signaling regulation of cytoplasmic pattern recognition receptor signaling pathway positive regulation of response to stimulus positive regulation of response to external stimulus endolysosomal toll-like receptor signaling pathway immune response-regulating signaling pathway regulation of intracellular signal transduction regulation of response to stress response to stress innate immune response response to external biotic stimulus regulation of toll-like receptor 3 signaling pathway regulation of signaling positive regulation of innate immune response defense response defense response to symbiont immune system process regulation of cell communication toll-like receptor 3 signaling pathway positive regulation of signaling developmental process cellular developmental process hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell activation cell differentiation anatomical structure development T cell differentiation leukocyte differentiation immune response-regulating cell surface receptor signaling pathway negative regulation of signaling regulation of antigen receptor-mediated signaling pathway negative regulation of antigen receptor-mediated signaling pathway negative regulation of cell communication cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway negative regulation of response to stimulus regulation of T cell receptor signaling pathway T cell receptor signaling pathway negative regulation of signal transduction negative regulation of T cell receptor signaling pathway negative regulation of immune system process antigen receptor-mediated signaling pathway negative regulation of catabolic process regulation of catabolic process regulation of autophagy negative regulation of autophagy negative regulation of interleukin-8 production interleukin-8 production regulation of interleukin-8 production regulation of protein modification process positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process protein K63-linked ubiquitination regulation of protein K63-linked ubiquitination positive regulation of protein modification process protein ubiquitination protein metabolic process protein modification process regulation of protein modification by small protein conjugation or removal positive regulation of protein K63-linked ubiquitination positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of protein polyubiquitination regulation of post-translational protein modification regulation of protein metabolic process protein polyubiquitination primary metabolic process positive regulation of protein polyubiquitination macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal positive regulation of type I interferon production type I interferon production positive regulation of multicellular organismal process positive regulation of cytokine production regulation of type I interferon production regulation of catalytic activity negative regulation of catalytic activity regulation of transferase activity regulation of MAP kinase activity negative regulation of kinase activity negative regulation of JNK cascade JNK cascade phosphate-containing compound metabolic process intracellular signaling cassette negative regulation of protein modification process phosphorus metabolic process negative regulation of protein metabolic process protein phosphorylation phosphorylation regulation of JNK cascade regulation of MAPK cascade regulation of molecular function regulation of kinase activity negative regulation of protein phosphorylation regulation of protein serine/threonine kinase activity regulation of phosphorus metabolic process regulation of protein phosphorylation negative regulation of intracellular signal transduction negative regulation of phosphate metabolic process negative regulation of protein serine/threonine kinase activity negative regulation of JUN kinase activity negative regulation of molecular function negative regulation of MAP kinase activity regulation of protein kinase activity negative regulation of protein kinase activity negative regulation of phosphorus metabolic process regulation of JUN kinase activity MAPK cascade regulation of phosphorylation negative regulation of phosphorylation negative regulation of MAPK cascade cell surface toll-like receptor signaling pathway regulation of toll-like receptor 4 signaling pathway positive regulation of toll-like receptor 4 signaling pathway innate immune response activating cell surface receptor signaling pathway cell surface pattern recognition receptor signaling pathway toll-like receptor 4 signaling pathway negative regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway negative regulation of cytoplasmic pattern recognition receptor signaling pathway nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway nucleotide-binding oligomerization domain containing 2 signaling pathway regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway positive regulation of ERK1 and ERK2 cascade positive regulation of MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade negative regulation of p38MAPK cascade p38MAPK cascade regulation of p38MAPK cascade regulation of leukocyte activation regulation of cell activation leukocyte proliferation lymphocyte proliferation regulation of natural killer cell activation regulation of lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation natural killer cell activation natural killer cell proliferation mononuclear cell proliferation regulation of cell population proliferation regulation of mononuclear cell proliferation regulation of natural killer cell proliferation regulation of lymphocyte activation dephosphorylation phosphoanandamide dephosphorylation response to lipid cellular response to lipopolysaccharide lipopolysaccharide-mediated signaling pathway cellular response to biotic stimulus response to bacterium response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical cellular response to lipid response to molecule of bacterial origin lipid metabolic process cellular response to nitrogen compound cellular response to muramyl dipeptide response to muramyl dipeptide response to nitrogen compound non-canonical NF-kappaB signal transduction regulation of non-canonical NF-kappaB signal transduction regulation of NLRP3 inflammasome complex assembly positive regulation of NLRP3 inflammasome complex assembly cellular component biogenesis cellular component assembly inflammasome-mediated signaling pathway canonical inflammasome complex assembly positive regulation of inflammasome-mediated signaling pathway regulation of inflammasome-mediated signaling pathway NLRP3 inflammasome complex assembly inflammatory response regulation of cellular component organization positive regulation of cellular component organization cellular component organization regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly protein-containing complex assembly cellular component organization or biogenesis protein-containing complex organization positive regulation of cellular component biogenesis regulation of cellular component biogenesis negative regulation of lymphocyte activation leukocyte cell-cell adhesion negative regulation of cell adhesion cell adhesion cell-cell adhesion regulation of cell-cell adhesion regulation of cell adhesion regulation of T cell activation negative regulation of cell activation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of leukocyte activation regulation of type II interferon production type II interferon production positive regulation of type II interferon production regulation of B cell receptor signaling pathway B cell receptor signaling pathway	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm cell periphery cytoplasmic side of plasma membrane cytoplasmic side of membrane membrane plasma membrane side of membrane membrane-bounded organelle intracellular organelle organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm cell periphery cytoplasmic side of plasma membrane cytoplasmic side of membrane membrane plasma membrane side of membrane membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F, G, H	IPR001452	SH3 domain	Domain
E, F, G, H	IPR036028	SH3-like domain superfamily	Homologous Superfamily
E, F, G, H	IPR037781	SKAP family	Family
E, F, G, H	IPR001849	Pleckstrin homology domain	Domain
E, F, G, H	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR047170	Tyrosine-protein phosphatase non-receptor type 12/18/22	Family
A, B, C, D	IPR016130	Protein-tyrosine phosphatase, active site	Active Site
A, B, C, D	IPR047253	Tyrosine-protein phosphatase non-receptor type 22, catalytic domain	Domain
A, B, C, D	IPR003595	Protein-tyrosine phosphatase, catalytic	Domain
A, B, C, D	IPR029021	Protein-tyrosine phosphatase-like	Homologous Superfamily
A, B, C, D	IPR016276	Non-receptor tyrosine-protein phosphatase 22	Family
A, B, C, D	IPR000242	Tyrosine-specific protein phosphatase, PTPase domain	Domain
A, B, C, D	IPR000387	Tyrosine-specific protein phosphatases domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F, G, H	Pharos: O75563	Crohn disease Liver Cirrhosis, Experimental osteosarcoma pancreatic intraductal papillary-mucinous carcinoma pituitary cancer Sjogren syndrome astrocytic tumor glioblastoma large cell medulloblastoma lung carcinoma malignant mesothelioma myopathy ovarian cancer pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor Crohn disease Liver Cirrhosis, Experimental osteosarcoma pancreatic intraductal papillary-mucinous carcinoma pituitary cancer Sjogren syndrome astrocytic tumor glioblastoma large cell medulloblastoma lung carcinoma malignant mesothelioma myopathy ovarian cancer pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor tuberculosis atypical teratoid rhabdoid tumor ductal breast carcinoma in situ invasive ductal breast carcinoma lymphoplasmacytic lymphoma malignant pancreatic neoplasm oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis breast cancer gastric carcinoma juvenile dermatomyositis lung cancer malignant ependymoma medulloblastoma
A, B, C, D	Pharos: Q9Y2R2	rheumatoid arthritis systemic lupus erythematosus Graves disease vitiligo autoimmune disease type 1 diabetes mellitus systemic sclerosis juvenile idiopathic arthritis temporal arteritis inflammatory bowel disease oligoarticular juvenile idiopathic arthritis Hashimoto thyroiditis IDDM 1 Crohn disease granulomatosis with polyangiitis rheumatoid arthritis systemic lupus erythematosus Graves disease vitiligo autoimmune disease type 1 diabetes mellitus systemic sclerosis juvenile idiopathic arthritis temporal arteritis inflammatory bowel disease oligoarticular juvenile idiopathic arthritis Hashimoto thyroiditis IDDM 1 Crohn disease granulomatosis with polyangiitis Vogt-Koyanagi-Harada disease hypothyroidism Libman-Sacks Disease acquired metabolic disease lupus erythematosus myasthenia gravis diabetes mellitus scleroderma interstitial cystitis lung cancer alopecia areata B-cell chronic lymphocytic leukemia myocardial infarction pancreatic intraductal papillary-mucinous neoplasm diffuse scleroderma Sjogren syndrome ulcerative colitis heart disease IgA glomerulonephritis lung carcinoma arthritic joint disease malignant mesothelioma breast carcinoma myositis cutaneous lupus erythematosus psoriasis rheumatoid factor-negative juvenile idiopathic arthritis ductal breast carcinoma in situ skin basal cell carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E, F, G, H	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.