1V1T

Crystal structure of the PDZ tandem of human syntenin in complex with TNEYKV 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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1v1ta1	All beta proteins	PDZ domain-like	PDZ domain-like	PDZ domain	Syntenin 1	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1v1ta3	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1v1tb1	All beta proteins	PDZ domain-like	PDZ domain-like	PDZ domain	Syntenin 1	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1v1tb3	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	e1v1tA1	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ	ECOD (1.6)
B	PDZ	e1v1tB1	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

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 cellular biosynthetic process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic 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 regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process 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 regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic 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 [auth S], D [auth T]	TNEYKV PEPTIDE	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR051230	Amyloid-beta A4 Precursor Protein-Binding	Family
A, B	IPR036034	PDZ superfamily	Homologous Superfamily
A, B	IPR001478	PDZ domain	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

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.