1YBO

Crystal structure of the PDZ tandem of human syntenin with syndecan peptide

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1yboa1	All beta proteins	PDZ domain-like	PDZ domain-like	PDZ domain	Syntenin 1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1yboa3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1ybob1	All beta proteins	PDZ domain-like	PDZ domain-like	PDZ domain	Syntenin 1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1ybob3	Artifacts	Tags	Tags	Tags	N-terminal Tags	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	PDZ domain-like	8040399	3000388	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PDZ domain-like	8040399	3000388	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	PDZ	e1yboA1	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ	ECOD (1.6)
B	PDZ	e1yboB1	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
B	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00595	PDZ domain (PDZ)	PDZ domain	PDZ domains are found in diverse signaling proteins.	Domain
C, D	PF01034	Syndecan domain (Syndecan)	Syndecan domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Syntenin 1	protein binding binding signaling receptor binding G protein-coupled receptor binding frizzled binding protein-containing complex binding ephrin receptor binding interleukin-5 receptor binding cytokine receptor binding growth factor receptor binding neurexin family protein binding identical protein binding cell adhesion molecule binding protein heterodimerization activity protein binding binding signaling receptor binding G protein-coupled receptor binding frizzled binding protein-containing complex binding ephrin receptor binding interleukin-5 receptor binding cytokine receptor binding growth factor receptor binding neurexin family protein binding identical protein binding cell adhesion molecule binding protein heterodimerization activity protein dimerization activity ionotropic glutamate receptor binding glutamate receptor binding molecular sequestering activity protein sequestering activity syndecan binding proteoglycan binding carbohydrate derivative binding growth factor binding ion binding phosphatidylinositol-4,5-bisphosphate binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding small molecule binding protein-macromolecule adaptor activity cytoskeletal anchor activity molecular adaptor activity	regulation of localization import into cell regulation of cellular process regulation of cellular component organization receptor internalization transport negative regulation of biological process negative regulation of transport negative regulation of endocytosis regulation of receptor internalization vesicle-mediated transport cellular component organization localization negative regulation of cellular process regulation of localization import into cell regulation of cellular process regulation of cellular component organization receptor internalization transport negative regulation of biological process negative regulation of transport negative regulation of endocytosis regulation of receptor internalization vesicle-mediated transport cellular component organization localization negative regulation of cellular process cellular component organization or biogenesis regulation of endocytosis regulation of biological process negative regulation of cellular component organization regulation of transport negative regulation of receptor-mediated endocytosis regulation of receptor-mediated endocytosis biological regulation regulation of vesicle-mediated transport establishment of localization cellular process endocytosis receptor-mediated endocytosis negative regulation of receptor internalization protein localization establishment of protein localization cellular localization establishment of protein localization to membrane protein targeting localization within membrane protein localization to membrane protein targeting to membrane cellular macromolecule localization macromolecule localization organelle organization actin cytoskeleton organization actin filament-based process cytoskeleton organization cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette signal transduction positive regulation of cellular process regulation of signaling positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication positive regulation of signaling trans-synaptic signaling synaptic signaling anterograde trans-synaptic signaling cell-cell signaling chemical synaptic transmission negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process developmental process multicellular organismal process presynapse organization nervous system development cellular component biogenesis multicellular organism development cell junction organization cellular component assembly cell junction assembly anatomical structure development synapse organization synapse assembly presynapse assembly system development regulation of growth growth positive regulation of cell growth regulation of cell growth cell growth positive regulation of growth regulation of mitotic cell cycle cell cycle regulation of cell cycle mitotic cell cycle cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of transforming growth factor beta receptor signaling pathway cellular response to endogenous stimulus enzyme-linked receptor protein signaling pathway cell surface receptor signaling pathway regulation of cellular response to transforming growth factor beta stimulus response to endogenous stimulus positive regulation of transforming growth factor beta receptor signaling pathway regulation of cellular response to growth factor stimulus positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of cellular response to transforming growth factor beta stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway regulation of epithelial to mesenchymal transition regulation of developmental process cellular developmental process positive regulation of epithelial to mesenchymal transition regulation of cell differentiation mesenchyme development positive regulation of developmental process positive regulation of cell differentiation cell differentiation regulation of multicellular organismal process animal organ development tissue development epithelial to mesenchymal transition positive regulation of multicellular organismal process mesenchymal cell differentiation substrate-dependent cell migration, cell extension plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly substrate-dependent cell migration cell migration cell motility cell projection assembly small GTPase-mediated signal transduction Ras protein signal transduction cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration locomotion exosomal secretion establishment of organelle localization positive regulation of secretion by cell positive regulation of exosomal secretion positive regulation of exocytosis secretion by cell regulation of secretion by cell positive regulation of secretion organelle localization establishment of localization in cell vesicle localization positive regulation of cellular component biogenesis secretion regulation of exosomal secretion establishment of vesicle localization export from cell regulation of cellular component biogenesis extracellular exosome biogenesis regulation of secretion exocytosis positive regulation of transport extracellular vesicle biogenesis regulation of exocytosis positive regulation of phosphorylation positive regulation of phosphorus metabolic process phosphorylation positive regulation of cellular metabolic process positive regulation of phosphate metabolic process positive regulation of metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process regulation of phosphorus metabolic process regulation of phosphorylation phosphorus metabolic process positive regulation of extracellular exosome assembly positive regulation of organelle organization positive regulation of cellular component organization regulation of extracellular exosome assembly vesicle organization extracellular exosome assembly organelle assembly regulation of organelle organization regulation of organelle assembly positive regulation of organelle assembly	membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane extracellular exosome membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytoplasm cytosol cell periphery protein-containing complex interleukin-5 receptor complex plasma membrane protein complex plasma membrane plasma membrane signaling receptor complex membrane protein complex receptor complex cell-cell junction adherens junction anchoring junction cell junction cytoskeleton intracellular non-membrane-bounded organelle non-membrane-bounded organelle focal adhesion cell-substrate junction pigment granule intracellular vesicle melanosome cytoplasmic vesicle membrane microdomain membrane raft presynapse synapse lytic vacuole membrane-enclosed lumen cytoplasmic vesicle lumen vacuolar lumen intracellular organelle lumen lysosome vesicle lumen azurophil granule vacuole secretory granule lumen azurophil granule lumen organelle lumen secretory granule primary lysosome secretory vesicle nucleoplasm nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane blood microparticle
C, D	Syndecan-4	molecular transducer activity signaling receptor activity thrombospondin receptor activity protein binding binding fibronectin binding kinase binding protein kinase C binding enzyme binding protein kinase binding identical protein binding	negative regulation of lymphocyte proliferation multicellular organismal process regulation of cellular process regulation of leukocyte activation negative regulation of biological process regulation of cell activation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation T cell activation lymphocyte proliferation regulation of immune system process regulation of leukocyte proliferation regulation of biological process negative regulation of lymphocyte proliferation multicellular organismal process regulation of cellular process regulation of leukocyte activation negative regulation of biological process regulation of cell activation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation T cell activation lymphocyte proliferation regulation of immune system process regulation of leukocyte proliferation regulation of biological process cell population proliferation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion regulation of cell population proliferation mononuclear cell proliferation negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of multicellular organismal process negative regulation of leukocyte activation lymphocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation negative regulation of mononuclear cell proliferation cell adhesion cell-cell adhesion negative regulation of cellular process regulation of multicellular organismal process regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation negative regulation of cell population proliferation regulation of cell adhesion biological regulation cell activation regulation of T cell activation negative regulation of cell activation regulation of T cell proliferation negative regulation of immune system process immune system process regulation of mononuclear cell proliferation cellular process regulation of lymphocyte activation cell migration cell motility regulation of cellular component organization positive regulation of cellular component organization cell-substrate junction assembly positive regulation of cell-substrate junction organization positive regulation of biological process cellular component organization cellular component biogenesis cellular component assembly cell junction assembly positive regulation of cell-substrate adhesion regulation of cell-substrate junction organization cellular component organization or biogenesis positive regulation of cellular process focal adhesion assembly positive regulation of focal adhesion assembly positive regulation of cellular component biogenesis regulation of cell-substrate adhesion positive regulation of cell adhesion cell-substrate adhesion positive regulation of cell-matrix adhesion regulation of cellular component biogenesis regulation of cell junction assembly positive regulation of cell junction assembly cell junction organization cell-matrix adhesion regulation of cell-matrix adhesion cell-substrate junction organization regulation of focal adhesion assembly regulation of cell-substrate junction assembly regulation of cell motility regulation of fibroblast migration fibroblast migration regulation of locomotion ameboidal-type cell migration regulation of cell migration locomotion embryonic epithelial tube formation chordate embryonic development tube formation embryo development multicellular organism development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching anatomical structure development epithelial tube morphogenesis system development developmental process morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium nervous system development tissue development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure ureteric bud development mesonephric epithelium development kidney epithelium development mesonephros development animal organ development renal system development kidney development mesonephric tubule development inner ear receptor cell development cellular developmental process cell projection organization sensory organ development cell development neuron projection development neurogenesis neuron differentiation cell differentiation inner ear development mechanoreceptor differentiation plasma membrane bounded cell projection organization ear development inner ear receptor cell differentiation generation of neurons neuron development inner ear receptor cell stereocilium organization wound healing response to stimulus response to stress response to wounding exosomal secretion establishment of organelle localization regulation of localization cellular localization transport positive regulation of secretion by cell positive regulation of exosomal secretion vesicle-mediated transport positive regulation of exocytosis localization secretion by cell regulation of secretion by cell positive regulation of secretion organelle localization establishment of localization in cell vesicle localization secretion regulation of transport regulation of exosomal secretion establishment of vesicle localization export from cell regulation of vesicle-mediated transport establishment of localization extracellular exosome biogenesis regulation of secretion exocytosis positive regulation of transport extracellular vesicle biogenesis regulation of exocytosis positive regulation of extracellular exosome assembly positive regulation of organelle organization regulation of extracellular exosome assembly vesicle organization extracellular exosome assembly organelle assembly regulation of organelle organization organelle organization regulation of organelle assembly positive regulation of organelle assembly regulation of cytoskeleton organization regulation of actin filament-based process regulation of actin filament bundle assembly positive regulation of actin filament bundle assembly actin filament bundle organization positive regulation of stress fiber assembly actin filament-based process stress fiber assembly regulation of actin filament organization actin cytoskeleton organization actomyosin structure organization positive regulation of cytoskeleton organization actin filament organization positive regulation of supramolecular fiber organization regulation of stress fiber assembly contractile actin filament bundle assembly regulation of actomyosin structure organization actin filament bundle assembly regulation of actin cytoskeleton organization regulation of supramolecular fiber organization supramolecular fiber organization cytoskeleton organization	anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cytoplasm lysosome extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cell surface costamere intracellular non-membrane-bounded organelle contractile muscle fiber supramolecular fiber myofibril supramolecular polymer supramolecular complex non-membrane-bounded organelle cell periphery plasma membrane membrane Golgi apparatus endomembrane system Golgi lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036034	PDZ superfamily	Homologous Superfamily
A, B	IPR001478	PDZ domain	Domain
C, D	IPR027789	Syndecan/Neurexin domain	Domain
C, D	IPR030479	Syndecan, conserved site	Conserved Site
C, D	IPR001050	Syndecan	Family
C, D	IPR003585	Neurexin/syndecan/glycophorin C	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: O00560	astrocytic tumor diabetes mellitus gallbladder disease lung cancer osteoarthritis ovarian cancer cholelithiasis Duchenne muscular dystrophy glioblastoma lung carcinoma osteoarthritis susceptibility 1 subependymal giant cell astrocytoma dermatomyositis Emery-Dreifuss muscular dystrophy large cell medulloblastoma astrocytic tumor diabetes mellitus gallbladder disease lung cancer osteoarthritis ovarian cancer cholelithiasis Duchenne muscular dystrophy glioblastoma lung carcinoma osteoarthritis susceptibility 1 subependymal giant cell astrocytoma dermatomyositis Emery-Dreifuss muscular dystrophy large cell medulloblastoma lymphoplasmacytic lymphoma Osteoarthrosis Deformans
C, D	Pharos: P31431	non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor Sjogren syndrome adrenal cortex carcinoma cutaneous lupus erythematosus facioscapulohumeral muscular dystrophy interstitial cystitis lung cancer medulloblastoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis tuberculosis atypical teratoid rhabdoid tumor non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor Sjogren syndrome adrenal cortex carcinoma cutaneous lupus erythematosus facioscapulohumeral muscular dystrophy interstitial cystitis lung cancer medulloblastoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis tuberculosis atypical teratoid rhabdoid tumor diabetes mellitus Gaucher disease invasive ductal breast carcinoma malignant glioma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma sinusitis breast cancer esophageal adenocarcinoma glioblastoma large cell medulloblastoma malignant pancreatic neoplasm ovarian cancer

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.