7A2X

Crystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R123H mutant in complex with VSL12 at pH 5.0

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	SH3-domain	8041562	3000153	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	SH3_1	e7a2xA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00018	SH3 domain (SH3_1)	SH3 domain	SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase Swiss:P12931. The structure is a partly opened beta barrel.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Tyrosine-protein kinase Fyn	protein tyrosine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups cytoskeletal protein binding protein binding binding tubulin binding alpha-tubulin binding adenyl ribonucleotide binding protein tyrosine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups cytoskeletal protein binding protein binding binding tubulin binding alpha-tubulin binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding non-membrane spanning protein tyrosine kinase activity signaling receptor binding ephrin receptor binding cation binding metal ion binding growth factor receptor binding scaffold protein binding type 5 metabotropic glutamate receptor binding glutamate receptor binding G protein-coupled receptor binding G protein-coupled glutamate receptor binding tau-protein kinase activity tau protein binding identical protein binding phospholipase binding enzyme binding transmembrane transporter binding enzyme regulator activity enzyme activator activity molecular function activator activity phospholipase activator activity molecular function regulator activity lipase activator activity disordered domain specific binding protein domain specific binding	regulation of calcium ion transport regulation of localization import into cell regulation of cellular process transport monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport calcium ion import into cytosol regulation of calcium ion transport regulation of localization import into cell regulation of cellular process transport monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport calcium ion import into cytosol monoatomic cation transport regulation of metal ion transport regulation of calcium ion import regulation of biological process calcium ion transmembrane import into cytosol regulation of transport regulation of monoatomic ion transport import across plasma membrane biological regulation inorganic ion transmembrane transport establishment of localization inorganic cation import across plasma membrane inorganic cation transmembrane transport transmembrane transport regulation of transmembrane transport calcium ion import across plasma membrane regulation of calcium ion import across plasma membrane inorganic ion import across plasma membrane cellular process regulation of monoatomic cation transmembrane transport calcium ion import calcium ion transmembrane transport regulation of catalytic activity positive regulation of protein metabolic process positive regulation of peptidase activity positive regulation of biological process regulation of primary metabolic process positive regulation of molecular function positive regulation of metabolic process regulation of proteolysis proteolysis regulation of endopeptidase activity positive regulation of macromolecule metabolic process protein metabolic process regulation of cysteine-type endopeptidase activity regulation of protein metabolic process regulation of peptidase activity positive regulation of catalytic activity primary metabolic process regulation of macromolecule metabolic process regulation of molecular function positive regulation of hydrolase activity positive regulation of cysteine-type endopeptidase activity regulation of hydrolase activity positive regulation of endopeptidase activity positive regulation of proteolysis metabolic process macromolecule metabolic process regulation of metabolic process catabolic process protein catabolic process macromolecule catabolic process regulation of neuron projection development multicellular organismal process regulation of cellular component organization positive regulation of cellular component organization cellular developmental process cell projection organization cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation positive regulation of neuron projection development cell differentiation anatomical structure development positive regulation of cell projection organization cellular component organization or biogenesis positive regulation of cellular process system development developmental process plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization protein phosphorylation phosphorylation cellular metabolic process macromolecule modification phosphate-containing compound metabolic process protein modification process phosphorus metabolic process regulation of defense response response to stimulus regulation of response to external stimulus negative regulation of inflammatory response negative regulation of biological process inflammatory response to antigenic stimulus response to stress regulation of response to stress regulation of immune system process negative regulation of inflammatory response to antigenic stimulus defense response immune response negative regulation of response to stimulus negative regulation of immune response regulation of inflammatory response to antigenic stimulus response to external stimulus regulation of inflammatory response regulation of response to stimulus negative regulation of immune system process immune system process negative regulation of response to external stimulus negative regulation of defense response regulation of immune response inflammatory response response to oxidative stress response to singlet oxygen response to chemical response to oxygen-containing compound response to reactive oxygen species detection of external stimulus detection of stimulus involved in sensory perception of pain system process detection of mechanical stimulus involved in sensory perception of pain nervous system process response to mechanical stimulus sensory perception of pain detection of mechanical stimulus involved in sensory perception sensory perception of mechanical stimulus detection of abiotic stimulus detection of stimulus sensory perception detection of mechanical stimulus response to abiotic stimulus detection of stimulus involved in sensory perception reactive oxygen species biosynthetic process cellular biosynthetic process reactive oxygen species metabolic process negative regulation of cellular metabolic process negative regulation of reactive oxygen species metabolic process negative regulation of reactive oxygen species biosynthetic process regulation of hydrogen peroxide metabolic process negative regulation of cellular process regulation of biosynthetic process regulation of hydrogen peroxide biosynthetic process negative regulation of metabolic process hydrogen peroxide metabolic process regulation of cellular metabolic process hydrogen peroxide biosynthetic process regulation of reactive oxygen species biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process negative regulation of hydrogen peroxide metabolic process biosynthetic process negative regulation of biosynthetic process negative regulation of hydrogen peroxide biosynthetic process regulation of reactive oxygen species metabolic process head development forebrain development animal organ development brain development central nervous system development dendritic spine maintenance dendritic spine organization postsynapse organization cellular component maintenance cell junction organization neuron projection organization synapse organization gene expression macromolecule biosynthetic process axonogenesis plasma membrane bounded cell projection morphogenesis cell morphogenesis cell projection morphogenesis neuron projection morphogenesis axon guidance axon development cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron projection guidance leukocyte migration cell migration cell motility cellular response to stimulus signaling signal transduction intracellular signal transduction cell communication negative regulation of macromolecule metabolic process regulation of gene expression negative regulation of gene expression negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of signaling cell surface receptor signaling pathway regulation of signal transduction glutamate receptor signaling pathway regulation of glutamate receptor signaling pathway regulation of cell communication cell surface receptor protein tyrosine kinase signaling pathway vascular endothelial growth factor receptor signaling pathway enzyme-linked receptor protein signaling pathway cellular response to nitrogen compound response to nitrogen compound cellular response to amyloid-beta cellular response to oxygen-containing compound cellular response to chemical stimulus response to amyloid-beta immune response-regulating cell surface receptor signaling pathway involved in phagocytosis immune response-regulating cell surface receptor signaling pathway Fc-gamma receptor signaling pathway involved in phagocytosis vesicle-mediated transport positive regulation of response to stimulus immune response-activating signaling pathway Fc receptor signaling pathway immune response-regulating signaling pathway positive regulation of immune response phagocytosis Fc-gamma receptor signaling pathway positive regulation of immune system process immune response-activating cell surface receptor signaling pathway Fc receptor mediated stimulatory signaling pathway immune effector process endocytosis activation of immune response behavior learning learning or memory cognition adaptive immune response negative regulation of post-translational protein modification regulation of protein modification process regulation of protein ubiquitination protein ubiquitination negative regulation of protein modification process negative regulation of protein ubiquitination regulation of protein modification by small protein conjugation or removal negative regulation of protein metabolic process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal ephrin receptor signaling pathway regulation of protein phosphorylation peptidyl-tyrosine modification regulation of phosphate metabolic process peptidyl-amino acid modification regulation of peptidyl-tyrosine phosphorylation regulation of phosphorylation regulation of phosphorus metabolic process peptidyl-tyrosine phosphorylation biological process involved in interspecies interaction between organisms response to other organism defense response to symbiont response to biotic stimulus defense response to other organism innate immune response response to external biotic stimulus protein localization cellular localization regulation of protein localization positive regulation of protein localization to membrane localization within membrane protein localization to membrane regulation of cellular localization cellular macromolecule localization macromolecule localization positive regulation of protein localization regulation of protein localization to membrane trans-synaptic signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling cellular response to acid chemical cellular response to amino acid stimulus cellular response to L-glutamate response to amino acid response to acid chemical response to L-glutamate reelin-mediated signaling pathway regulation of dendritic spine maintenance regulation of synapse structure or activity regulation of biological quality negative regulation of cell projection organization negative regulation of dendritic spine maintenance negative regulation of cellular component organization regulation of postsynapse organization regulation of synapse organization G protein-coupled glutamate receptor signaling pathway G protein-coupled receptor signaling pathway 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 adhesion cell-cell adhesion T cell activation positive regulation of leukocyte activation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation lymphocyte costimulation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process T cell costimulation regulation of lymphocyte activation negative regulation of catabolic process regulation of catabolic process negative regulation of protein catabolic process regulation of protein catabolic process establishment of protein localization protein targeting positive regulation of establishment of protein localization regulation of protein targeting to membrane establishment of protein localization to membrane regulation of establishment of protein localization protein targeting to membrane regulation of protein targeting positive regulation of protein targeting to membrane positive regulation of protein localization to nucleus regulation of protein localization to nucleus protein localization to nucleus protein localization to organelle T cell receptor signaling pathway antigen receptor-mediated signaling pathway cellular response to endogenous stimulus cellular response to growth factor stimulus cellular response to platelet-derived growth factor stimulus response to endogenous stimulus response to growth factor response to platelet-derived growth factor response to transforming growth factor beta cellular response to transforming growth factor beta stimulus heart process circulatory system process dendrite development dendrite morphogenesis positive regulation of response to biotic stimulus innate immune response-activating signaling pathway regulation of innate immune response response to lectin cellular response to lectin positive regulation of defense response activation of innate immune response regulation of response to biotic stimulus innate immune response activating cell surface receptor signaling pathway positive regulation of response to external stimulus positive regulation of innate immune response stimulatory C-type lectin receptor signaling pathway feeding behavior response to alcohol response to ethanol regulation of developmental process regulation of cell shape regulation of cell morphogenesis regulation of anatomical structure morphogenesis cellular response to oxidative stress cellular response to chemical stress cellular response to hydrogen peroxide response to hydrogen peroxide cellular response to reactive oxygen species cellular response to stress intrinsic apoptotic signaling pathway in response to oxidative stress regulation of oxidative stress-induced intrinsic apoptotic signaling pathway negative regulation of signaling negative regulation of intracellular signal transduction regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway negative regulation of cell communication regulation of intracellular signal transduction negative regulation of apoptotic signaling pathway intrinsic apoptotic signaling pathway negative regulation of programmed cell death regulation of apoptotic process negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway cell death negative regulation of signal transduction 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 response to glycine cellular response to glycine positive regulation of phosphorylation positive regulation of phosphate metabolic process positive regulation of protein phosphorylation tyrosine phosphorylation of STAT protein positive regulation of phosphorus metabolic process cell surface receptor signaling pathway via STAT positive regulation of cellular metabolic process positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein modification process regulation of tyrosine phosphorylation of STAT protein positive regulation of tyrosine phosphorylation of STAT protein cell surface receptor signaling pathway via JAK-STAT neuron migration cell population proliferation leukocyte proliferation activated T cell proliferation mononuclear cell proliferation lymphocyte proliferation T cell proliferation	somatodendritic compartment cell body perikaryon neuronal cell body cellular anatomical entity intracellular anatomical structure cytoplasm cytosol polymeric cytoskeletal fiber actin filament actin cytoskeleton intracellular organelle cytoskeleton organelle somatodendritic compartment cell body perikaryon neuronal cell body cellular anatomical entity intracellular anatomical structure cytoplasm cytosol polymeric cytoskeletal fiber actin filament actin cytoskeleton intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle supramolecular fiber supramolecular polymer supramolecular complex non-membrane-bounded organelle cell periphery plasma membrane membrane membrane microdomain membrane raft membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system cytoplasmic vesicle vesicle Schaffer collateral - CA1 synapse synapse cell junction cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection perinuclear endoplasmic reticulum perinuclear region of cytoplasm endoplasmic reticulum mitochondrion glial cell projection postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization asymmetric synapse nucleus
B	VSL12 high affinity synthetic peptide acetylated in the amino-terminus	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A	IPR000719	Protein kinase domain	Domain
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR036860	SH2 domain superfamily	Homologous Superfamily
A	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A	IPR035750	Fyn/Yrk, SH3 domain	Domain
A	IPR008266	Tyrosine-protein kinase, active site	Active Site
A	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A	IPR001452	SH3 domain	Domain
A	IPR047924	Fyn/Yrk, SH2 domain	Domain
A	IPR000980	SH2 domain	Domain
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR050198	Non-receptor tyrosine kinases involved in cell signaling	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P06241	adult T-cell leukemia/lymphoma Liver Cirrhosis, Experimental mature T-cell and NK-cell non-Hodgkin lymphoma psoriasis gastric neoplasm Sjogren syndrome hereditary diffuse gastric adenocarcinoma tuberculosis invasive ductal breast carcinoma acute T cell leukemia malignant mesothelioma attention deficit hyperactivity disorder, inattentive type non-small cell lung carcinoma pancreatic ductal adenocarcinoma cystic fibrosis adult T-cell leukemia/lymphoma Liver Cirrhosis, Experimental mature T-cell and NK-cell non-Hodgkin lymphoma psoriasis gastric neoplasm Sjogren syndrome hereditary diffuse gastric adenocarcinoma tuberculosis invasive ductal breast carcinoma acute T cell leukemia malignant mesothelioma attention deficit hyperactivity disorder, inattentive type non-small cell lung carcinoma pancreatic ductal adenocarcinoma cystic fibrosis esophageal adenocarcinoma pulmonary hypertension glioblastoma skin disease idiopathic interstitial pneumonia ulcerative colitis juvenile dermatomyositis lung cancer medulloblastoma B-cell chronic lymphocytic leukemia oligodendroglioma breast fibroadenoma pancreatic intraductal papillary-mucinous neoplasm Down syndrome psoriatic arthritis gastric cancer schizophrenia Hashimoto thyroiditis squamous cell lung carcinoma interstitial cystitis large cell medulloblastoma lymphoplasmacytic lymphoma alcohol abuse malignant pancreatic neoplasm astrocytic tumor metastatic melanoma bipolar disorder ovarian cancer cancer pilocytic astrocytoma ductal breast carcinoma in situ pulmonary fibrosis

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359

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.