6RLC | pdb_00006rlc

Crystal structure of the PDZ tandem of syntenin in complex with fragment F13

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	PDZ domain-like	8040399	3000388	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PDZ domain-like	8040399	3000388	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PDZ domain-like	8040399	3000388	SCOP2B (2022-06-29)
A	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)
D	PG_binding_1	e6rlcD1	A: alpha bundles	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F: PG_binding_1	ECOD (develop294)
C	PG_binding_1	e6rlcC1	A: alpha bundles	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F: PG_binding_1	ECOD (develop294)
B	PG_binding_1	e6rlcB1	A: alpha bundles	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F: PG_binding_1	ECOD (develop294)
A	PG_binding_1	e6rlcA1	A: alpha bundles	X: cradle loop barrel	H: N-terminal domain of poxin	T: N-terminal domain of poxin	F: PG_binding_1	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, C, D	Syntenin-1	protein binding binding signaling receptor binding G protein-coupled receptor binding frizzled binding interleukin-5 receptor binding cytokine receptor binding growth factor receptor binding identical protein binding protein heterodimerization activity protein dimerization activity molecular sequestering activity protein sequestering activity syndecan binding protein binding binding signaling receptor binding G protein-coupled receptor binding frizzled binding interleukin-5 receptor binding cytokine receptor binding growth factor receptor binding identical protein binding protein heterodimerization activity protein dimerization activity molecular sequestering activity protein sequestering activity syndecan binding proteoglycan binding carbohydrate derivative 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 establishment of protein localization cellular localization establishment of protein localization to membrane protein targeting localization within membrane protein targeting to membrane 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 RNA 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 negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic 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 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 multicellular organismal process 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 anatomical structure development regulation of multicellular organismal process developmental 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 cellular component biogenesis cellular component 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 phosphate metabolic process positive regulation of 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	cellular anatomical structure membrane 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 cellular anatomical structure membrane 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 membraneless organelle intracellular membraneless organelle focal adhesion cell-substrate junction pigment granule intracellular vesicle melanosome cytoplasmic vesicle membrane microdomain membrane raft 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 synapse

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.