6AK2 | pdb_00006ak2

Crystal structure of the syntenin PDZ1 domain in complex with the peptide inhibitor KSL-128018

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Hydrolase	e6ak2B1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: Hydrolase	ECOD (v294.1)
A	TSP_1	e6ak2A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Ntn	T: Proteasome subunits	F: TSP_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

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

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
C [auth D], D [auth E]	peptide inhibitor KSL-128018	-	-	-
A, B	Syntenin-1	cell adhesion molecule binding protein binding binding protein heterodimerization activity protein dimerization activity ionotropic glutamate receptor binding signaling receptor binding glutamate receptor binding molecular sequestering activity protein sequestering activity G protein-coupled receptor binding frizzled binding syndecan binding proteoglycan binding cell adhesion molecule binding protein binding binding protein heterodimerization activity protein dimerization activity ionotropic glutamate receptor binding signaling receptor binding glutamate receptor binding molecular sequestering activity protein sequestering activity G protein-coupled receptor binding frizzled binding 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 small molecule 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	regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of mitotic cell cycle cell cycle regulation of cell cycle mitotic cell cycle cellular response to stimulus positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway positive regulation of signal transduction cellular response to growth factor stimulus response to stimulus signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of signal transduction cell communication regulation of transforming growth factor beta receptor signaling pathway positive regulation of response to stimulus cellular response to endogenous stimulus signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling 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 regulation of response to stimulus transforming growth factor beta receptor signaling pathway regulation of cell communication response to growth factor transforming growth factor beta receptor superfamily signaling pathway positive regulation of signaling 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 regulation of localization import into cell receptor internalization transport negative regulation of biological process negative regulation of transport negative regulation of endocytosis regulation of receptor internalization vesicle-mediated transport localization negative regulation of cellular process regulation of endocytosis negative regulation of cellular component organization regulation of transport negative regulation of receptor-mediated endocytosis regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization endocytosis receptor-mediated endocytosis negative regulation of receptor internalization small GTPase-mediated signal transduction Ras protein signal transduction intracellular signal transduction intracellular signaling cassette 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 cell migration cell motility locomotion exosomal secretion establishment of organelle localization cellular localization positive regulation of secretion by cell positive regulation of exosomal secretion positive regulation of exocytosis cellular component biogenesis 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 metabolic process regulation of phosphorus metabolic process regulation of phosphorylation phosphorus metabolic process regulation of metabolic process 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 regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription negative regulation of RNA 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 cellular component assembly extracellular exosome assembly organelle assembly regulation of organelle organization organelle organization regulation of organelle assembly positive regulation of organelle assembly presynapse organization nervous system development multicellular organism development cell junction organization cell junction assembly synapse organization synapse assembly presynapse assembly system development	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle nuclear membrane membrane nucleus endomembrane system organelle envelope nuclear envelope organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle cytosol cell periphery plasma membrane protein-containing complex interleukin-5 receptor complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex signaling receptor complex membrane microdomain membrane raft presynapse synapse membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane cell-cell junction adherens junction cytoskeleton membraneless organelle intracellular membraneless organelle

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

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.

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