5IBM

Structure of S502P, a Cancer-Associated Mutation of the Oncogenic Phosphatase SHP2

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5ibma3	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	Higher-molecular-weight phosphotyrosine protein phosphatases	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5ibma1	Alpha and beta proteins (a+b)	SH2-like	SH2 domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5ibmb3	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	Higher-molecular-weight phosphotyrosine protein phosphatases	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5ibmb1	Alpha and beta proteins (a+b)	SH2-like	SH2 domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

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	8044348	3000304	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SH2 domain	8035713	3000197	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SH2 domain	8035711	3000197	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8044348	3000304	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SH2 domain	8035711	3000197	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SH2 domain	8035713	3000197	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	SH2	e5ibmA1	A: a+b two layers	X: SH2 (From Topology)	H: SH2 (From Topology)	T: SH2	F: SH2	ECOD (1.6)
A	Y_phosphatase	e5ibmA3	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	SH2	e5ibmB1	A: a+b two layers	X: SH2 (From Topology)	H: SH2 (From Topology)	T: SH2	F: SH2	ECOD (1.6)
B	Y_phosphatase	e5ibmB2	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)
A	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (4.3.0)
A	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (4.3.0)
B	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (4.3.0)
B	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	PF00017	SH2 domain (SH2)	SH2 domain	-	Domain
A, B	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
A, B	Tyrosine-protein phosphatase non-receptor type 11	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 peptide hormone receptor binding hormone receptor binding phosphoprotein 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 peptide hormone receptor binding hormone receptor binding phosphoprotein binding phosphotyrosine residue binding protein phosphorylated amino acid binding cell adhesion molecule binding cadherin binding molecular adaptor activity 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 signaling receptor complex adaptor activity protein-macromolecule adaptor activity signaling adaptor activity	developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication response to peptide response to chemical cellular response to cytokine stimulus cellular process signal transduction heart development circulatory system development cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of type I interferon production cytokine production negative regulation of cellular process regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process type I interferon production cellular metabolic process negative regulation of metabolic process negative regulation of cytokine production regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process regulation of type I interferon production atrioventricular canal development positive regulation of cell communication regulation of localization regulation of hormone secretion transport positive regulation of biological process positive regulation of secretion by cell hormone secretion localization positive regulation of hormone secretion regulation of secretion by cell secretion by cell positive regulation of secretion signal release regulation of biological quality positive regulation of cellular process regulation of signaling regulation of transport secretion regulation of hormone levels export from cell cell-cell signaling establishment of localization regulation of secretion positive regulation of transport regulation of cell communication hormone transport positive regulation of signaling multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells within a tissue anatomical structure homeostasis tissue homeostasis homeostasis of number of cells system process regulation of system process negative regulation of transport negative regulation of lipid localization regulation of glucocorticoid secretion regulation of steroid hormone secretion negative regulation of secretion negative regulation of cortisol secretion negative regulation of hormone secretion negative regulation of secretion by cell negative regulation of steroid hormone secretion cortisol secretion lipid transport regulation of corticosteroid hormone secretion endocrine hormone secretion lipid export from cell regulation of cortisol secretion negative regulation of corticosteroid hormone secretion glucocorticoid secretion regulation of endocrine process corticosteroid hormone secretion negative regulation of signaling steroid hormone secretion regulation of lipid transport organic hydroxy compound transport negative regulation of cell communication negative regulation of glucocorticoid secretion negative regulation of lipid transport lipid localization endocrine process regulation of lipid localization macromolecule localization cellular component organization plasma membrane bounded cell projection organization cell projection organization cellular component organization or biogenesis microvillus organization ear development sensory organ development inner ear development protein dephosphorylation dephosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway ephrin receptor signaling pathway negative regulation of cell adhesion mediated by integrin regulation of cell adhesion mediated by integrin regulation of cell adhesion negative regulation of cell adhesion cell adhesion cell adhesion mediated by integrin protein localization establishment of protein localization cellular localization nitrogen compound transport regulation of protein localization nucleocytoplasmic transport nuclear transport cellular macromolecule localization establishment of localization in cell regulation of protein export from nucleus nuclear export regulation of intracellular transport regulation of establishment of protein localization intracellular transport regulation of nucleocytoplasmic transport regulation of protein transport protein export from nucleus protein transport regulation of cellular localization regulation of intracellular protein transport intracellular protein transport ERBB signaling pathway axonogenesis cellular developmental process plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development platelet-derived growth factor receptor signaling pathway cellular response to nitrogen compound positive regulation of signal transduction response to peptide hormone regulation of signal transduction insulin receptor signaling pathway regulation of cellular response to insulin stimulus positive regulation of response to stimulus cellular response to endogenous stimulus response to hormone cellular response to hormone stimulus positive regulation of cellular response to insulin stimulus response to endogenous stimulus regulation of insulin receptor signaling pathway positive regulation of insulin receptor signaling pathway response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus regulation of response to stimulus response to insulin cellular response to insulin stimulus epidermal growth factor receptor signaling pathway cerebellum morphogenesis cerebellar cortex morphogenesis hindbrain morphogenesis cerebellar cortex development cerebellum development metencephalon development anatomical structure formation involved in morphogenesis cerebellar cortex formation hindbrain development regulation of peptide secretion negative regulation of peptide secretion peptide secretion amide transport regulation of peptide hormone secretion growth hormone secretion negative regulation of peptide hormone secretion regulation of growth hormone secretion regulation of peptide transport negative regulation of growth hormone secretion peptide transport peptide hormone secretion regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell-cell adhesion T cell activation positive regulation of leukocyte activation regulation of immune system process regulation of cell-cell adhesion positive regulation of immune system process positive regulation of T cell activation positive regulation of cell adhesion cell activation regulation of T cell activation immune system process lymphocyte costimulation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process T cell costimulation regulation of lymphocyte activation multicellular organism growth developmental growth growth DNA damage checkpoint signaling regulation of cell cycle phase transition negative regulation of cell cycle cell cycle phase transition intracellular signal transduction cellular response to stress response to stress negative regulation of cell cycle phase transition cell cycle regulation of cell cycle cell cycle process regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling DNA damage response signal transduction in response to DNA damage chemical homeostasis glucose homeostasis carbohydrate homeostasis regulation of cellular component organization protein-containing complex organization regulation of cellular component biogenesis cellular component biogenesis regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly hemopoiesis megakaryocyte differentiation myeloid cell differentiation megakaryocyte development myeloid cell development organ growth positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade face morphogenesis head morphogenesis face development body morphogenesis interleukin-6 production positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of interleukin-6 production regulation of interleukin-6 production positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of gene expression positive regulation of cytokine production positive regulation of cellular biosynthetic process hormone-mediated signaling pathway integrin-mediated signaling pathway hormone metabolic process reproductive process multicellular organismal reproductive process regulation of interferon-beta production interferon-beta production positive regulation of type I interferon production positive regulation of interferon-beta production negative regulation of protein transport establishment of protein localization to extracellular region negative regulation of establishment of protein localization protein secretion regulation of protein secretion negative regulation of protein secretion protein localization to extracellular region negative regulation of protein localization negative regulation of insulin secretion regulation of insulin secretion insulin secretion astrocyte differentiation gliogenesis glial cell differentiation Bergmann glial cell differentiation intestinal epithelial cell migration epithelium migration tissue migration ameboidal-type cell migration epithelial cell migration cell migration cell motility response to fibroblast growth factor cellular response to growth factor stimulus fibroblast growth factor receptor signaling pathway response to growth factor cellular response to fibroblast growth factor stimulus platelet morphogenesis platelet formation neurotrophin TRK receptor signaling pathway neurotrophin signaling pathway peptidyl-tyrosine dephosphorylation 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 biotic stimulus interferon-mediated signaling pathway cellular response to type I interferon regulation of response to stress innate immune response 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 regulation of response to cytokine stimulus defense response to other organism type I interferon-mediated signaling pathway regulation of immune response response to type I interferon neutral lipid metabolic process triglyceride metabolic process cellular lipid metabolic process glycerolipid metabolic process acylglycerol metabolic process lipid metabolic process ossification positive regulation of ossification regulation of ossification cellular response to epidermal growth factor stimulus response to epidermal growth factor regulation of cartilage development regulation of chondrocyte differentiation regulation of developmental process connective tissue development negative regulation of cartilage development negative regulation of chondrocyte differentiation regulation of cell differentiation skeletal system development negative regulation of cell differentiation regulation of multicellular organismal development negative regulation of developmental process tissue development chondrocyte differentiation cartilage development positive regulation of cell cycle mitotic cell cycle regulation of mitotic cell cycle positive regulation of mitotic cell cycle regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production genitalia development reproductive system development sex differentiation developmental process involved in reproduction reproductive structure development hexose transmembrane transport D-glucose import carbohydrate transport positive regulation of D-glucose transmembrane transport positive regulation of transmembrane transport regulation of D-glucose import positive regulation of D-glucose import transmembrane transport regulation of transmembrane transport D-glucose transmembrane transport regulation of D-glucose transmembrane transport monosaccharide transmembrane transport carbohydrate transmembrane transport regulation of protein modification process positive regulation of phosphorylation regulation of protein phosphorylation positive regulation of protein metabolic process peptidyl-tyrosine modification positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein modification process regulation of phosphate metabolic process peptidyl-amino acid modification positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process regulation of peptidyl-tyrosine phosphorylation regulation of phosphorylation regulation of phosphorus metabolic process peptidyl-tyrosine phosphorylation	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR016130	Protein-tyrosine phosphatase, active site	Active Site
A, B	IPR036860	SH2 domain superfamily	Homologous Superfamily
A, B	IPR003595	Protein-tyrosine phosphatase, catalytic	Domain
A, B	IPR000980	SH2 domain	Domain
A, B	IPR012152	Protein-tyrosine phosphatase, non-receptor type-6, -11	Family
A, B	IPR029021	Protein-tyrosine phosphatase-like	Homologous Superfamily
A, B	IPR000242	Tyrosine-specific protein phosphatase, PTPase domain	Domain
A, B	IPR000387	Tyrosine-specific protein phosphatases domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q06124	Noonan syndrome with multiple lentigines Noonan syndrome Costello syndrome cardiofaciocutaneous syndrome juvenile myelomonocytic leukemia metachondromatosis Ollier disease neuroblastoma astrocytic tumor fibrillary astrocytoma acute myeloid leukemia adenocarcinoma anaplastic astrocytoma pilocytic astrocytoma squamous cell carcinoma Noonan syndrome with multiple lentigines Noonan syndrome Costello syndrome cardiofaciocutaneous syndrome juvenile myelomonocytic leukemia metachondromatosis Ollier disease neuroblastoma astrocytic tumor fibrillary astrocytoma acute myeloid leukemia adenocarcinoma anaplastic astrocytoma pilocytic astrocytoma squamous cell carcinoma hereditary multiple osteochondromas protoplasmic astrocytoma childhood cerebral astrocytoma LEOPARD syndrome 1 subependymal giant cell astrocytoma tubular adenocarcinoma Neurodevelopmental Disorders gemistocytic astrocytoma Noonan syndrome 1 granular cell carcinoma juvenile pilocytic astrocytoma leukemia systemic lupus erythematosus malignant ependymoma myelodysplastic syndrome Down syndrome myositis neurofibromatosis type 1 glioblastoma heart disease pancreatic ductal adenocarcinoma breast carcinoma hydrops fetalis prostate carcinoma Charcot-Marie-Tooth disease large cell medulloblastoma cleft lip lung adenocarcinoma systemic sclerosis cribriform carcinoma malignant glioma dermatomyositis Gaucher disease oligodendroglioma hematologic disease osteogenesis imperfecta peripheral arterial disease cancer hypertrophic cardiomyopathy plasma cell myeloma congenital anemia Maffucci syndrome cribriform carcinoma of breast medulloblastoma diffuse astrocytoma multiple pterygium syndrome myocardial infarction hematopoietic and lymphoid system neoplasm osteosarcoma astrocytoma (excluding glioblastoma) hereditary spastic paraplegia Pick disease carcinoma of esophagus intellectual disability progressive supranuclear palsy cerebral astrocytoma rheumatoid arthritis chronic myelomonocytic leukemia

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.