4ZNX | pdb_00004znx

Crystal structure of the Fyn-SH3 domain in complex with the high affinity peptide APP12

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	SH3-domain	8041562	3000153	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SH3-domain	8041562	3000153	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SH3-domain	8041562	3000153	SCOP2B (2022-06-29)
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)
D	SH3_1	e4znxD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)
C	SH3_1	e4znxC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)
B	SH3_1	e4znxB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)
A	SH3_1	e4znxA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
C	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
B	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
A	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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
E, F, G, H	APP12	-	-	-
A, B, C, D	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 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 CD8 receptor binding growth factor receptor binding scaffold protein binding CD4 receptor binding type 5 metabotropic glutamate receptor binding glutamate receptor binding G protein-coupled receptor binding G protein-coupled glutamate receptor binding phosphatidylinositol 3-kinase binding peptide hormone receptor binding hormone receptor binding protein serine/threonine kinase activity tau-protein kinase activity tau protein binding protein-containing complex binding T cell receptor 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	response to stimulus response to chemical response to xenobiotic stimulus 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 response to stimulus response to chemical response to xenobiotic stimulus 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 establishment of localization inorganic cation import across plasma membrane 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 cellular response to stimulus cellular response to nitrogen compound response to endogenous stimulus response to peptide hormone cellular response to peptide hormone stimulus response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone cellular response to hormone stimulus catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic 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 positive regulation of biological process 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 macromolecule modification phosphate-containing compound metabolic process protein modification process phosphorus metabolic process regulation of defense response 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 reactive oxygen species negative regulation of extrinsic apoptotic signaling pathway in absence of ligand signal transduction in absence of ligand negative regulation of signaling signaling regulation of signal transduction regulation of programmed cell death negative regulation of cell communication extrinsic apoptotic signaling pathway negative regulation of signal transduction in absence of ligand cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of cellular process extrinsic apoptotic signaling pathway in absence of ligand signal transduction regulation of signaling cell surface receptor signaling pathway negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway in absence of ligand regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway 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 reactive oxygen species metabolic process negative regulation of reactive oxygen species metabolic process negative regulation of reactive oxygen species biosynthetic process regulation of hydrogen peroxide metabolic process regulation of biosynthetic process regulation of hydrogen peroxide biosynthetic process negative regulation of metabolic process hydrogen peroxide metabolic process hydrogen peroxide biosynthetic process regulation of reactive oxygen species 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 metabolic 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 regulation of developmental process angiogenesis regulation of vasculature development tube morphogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development regulation of multicellular organismal development blood vessel morphogenesis tube development negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis vasculature development circulatory system development negative regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis negative regulation of multicellular organismal process intracellular signal transduction 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 negative regulation of macromolecule metabolic process glutamate receptor signaling pathway regulation of glutamate receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway vascular endothelial growth factor receptor signaling pathway enzyme-linked receptor protein signaling pathway cellular response to amyloid-beta 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 regulation of primary metabolic process 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 regulation of protein metabolic process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal ephrin receptor signaling pathway cellular localization regulation of protein localization positive regulation of protein localization to membrane localization within membrane protein localization to membrane regulation of cellular localization macromolecule localization positive regulation of protein localization intracellular 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 cell activation natural killer cell activation lymphocyte activation leukocyte activation 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 leukocyte cell-cell adhesion 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 cell-cell adhesion positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion 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 protein catabolic process negative regulation of catabolic process regulation of 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 growth factor stimulus cellular response to platelet-derived growth factor 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 response to biotic stimulus innate immune response-activating signaling pathway response to other organism regulation of innate immune response response to lectin defense response to other organism cellular response to lectin positive regulation of defense response activation of innate immune response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms innate immune response activating cell surface receptor signaling pathway positive regulation of response to external stimulus innate immune response response to external biotic stimulus positive regulation of innate immune response defense response to symbiont stimulatory C-type lectin receptor signaling pathway positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction regulation of intracellular signal transduction intracellular signaling cassette positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling neuron apoptotic process negative regulation of neuron apoptotic process regulation of neuron apoptotic process feeding behavior response to alcohol response to ethanol regulation of cell shape regulation of cell 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 peptidyl-tyrosine modification peptidyl-amino acid modification peptidyl-tyrosine phosphorylation intrinsic apoptotic signaling pathway in response to oxidative stress regulation of oxidative stress-induced intrinsic apoptotic signaling pathway negative regulation of intracellular signal transduction regulation of intrinsic apoptotic signaling pathway intrinsic apoptotic signaling pathway negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway response to glycine cellular response to glycine neuron migration cell population proliferation leukocyte proliferation activated T cell proliferation mononuclear cell proliferation lymphocyte proliferation T cell proliferation	somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body intracellular anatomical structure cytoplasm cytosol polymeric cytoskeletal fiber actin filament intracellular membraneless organelle actin cytoskeleton intracellular organelle cytoskeleton somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body intracellular anatomical structure cytoplasm cytosol polymeric cytoskeletal fiber actin filament intracellular membraneless organelle actin cytoskeleton intracellular organelle cytoskeleton organelle membraneless organelle supramolecular fiber supramolecular polymer supramolecular complex 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 glutamatergic synapse perinuclear endoplasmic reticulum perinuclear region of cytoplasm endoplasmic reticulum postsynaptic density, intracellular component postsynaptic specialization postsynaptic specialization, intracellular component postsynaptic density postsynapse neuron to neuron synapse asymmetric synapse mitochondrion glial cell projection nucleus

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	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

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.