5A2P | pdb_00005a2p

THE COMPLEX STRUCTURE OF PDZ DOMAINS IN SYNTENIN-1 WITH 4L PEPTIDE

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)
D	DnaJ	e5a2pD1	A: alpha bundles	X: Thymine dioxygenase JBP1 DNA-binding domain-like	H: Oligo-peptide binding protein (OPPA) insertion domain	T: Oligo-peptide binding protein (OPPA) insertion domain	F: DnaJ	ECOD (develop294)
C	DnaJ	e5a2pC1	A: alpha bundles	X: Thymine dioxygenase JBP1 DNA-binding domain-like	H: Oligo-peptide binding protein (OPPA) insertion domain	T: Oligo-peptide binding protein (OPPA) insertion domain	F: DnaJ	ECOD (develop294)
B	DnaJ	e5a2pB1	A: alpha bundles	X: Thymine dioxygenase JBP1 DNA-binding domain-like	H: Oligo-peptide binding protein (OPPA) insertion domain	T: Oligo-peptide binding protein (OPPA) insertion domain	F: DnaJ	ECOD (develop294)
A	DnaJ	e5a2pA1	A: alpha bundles	X: Thymine dioxygenase JBP1 DNA-binding domain-like	H: Oligo-peptide binding protein (OPPA) insertion domain	T: Oligo-peptide binding protein (OPPA) insertion domain	F: DnaJ	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
C	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)
A	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, 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
E, F, G, H	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	regulation of biological process signaling biological regulation cell-cell signaling cellular process cell communication 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 regulation of biological process signaling biological regulation cell-cell signaling cellular process cell communication 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 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 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 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 regulation of actin cytoskeleton organization actin filament bundle assembly regulation of supramolecular fiber organization supramolecular fiber organization cytoskeleton organization	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell surface intracellular anatomical structure intracellular membraneless organelle intracellular organelle costamere organelle membraneless organelle contractile muscle fiber cytoplasm cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell surface intracellular anatomical structure intracellular membraneless organelle intracellular organelle costamere organelle membraneless organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex cell periphery plasma membrane membrane extracellular region
A, B, C, D	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 phosphatidylinositol 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 space 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 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
E, F, G, H	IPR027789	Syndecan/Neurexin domain	Domain
E, F, G, H	IPR030479	Syndecan, conserved site	Conserved Site
E, F, G, H	IPR001050	Syndecan	Family
E, F, G, H	IPR003585	Neurexin/syndecan/glycophorin C	Domain
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

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.