4RD9 | pdb_00004rd9

X-RAY STRUCTURE OF THE APO FORM OF THE AMYLOID PRECURSOR PROTEIN-LIKE PROTEIN 1 (APLP1) E2 DOMAIN

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	d4rd9b_	All alpha proteins	STAT-like	CAPPD, an extracellular domain of amyloid beta A4 protein	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4rd9a_	All alpha proteins	STAT-like	CAPPD, an extracellular domain of amyloid beta A4 protein	automated matches	automated matches	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)
B	SCOP2B Superfamily	CAPPD-like	8072399	3001286	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CAPPD-like	8072399	3001286	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)
B	Flavodoxin_2	e4rd9B1	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: Flavodoxin_2	ECOD (v294.1)
A	Flavodoxin_2	e4rd9A1	A: a/b three-layered sandwiches	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: Flavodoxin_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.20.120.770	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Amyloid precursor protein, E2 domain	CATH (4.3.0)
A	1.20.120.770	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Amyloid precursor protein, E2 domain	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Amyloid-like protein 1	cation binding transition metal ion binding ion binding binding metal ion binding small molecule binding alpha-2B adrenergic receptor binding protein binding adrenergic receptor binding signaling receptor binding G protein-coupled receptor binding alpha-2C adrenergic receptor binding alpha-2A adrenergic receptor binding heparin binding cation binding transition metal ion binding ion binding binding metal ion binding small molecule binding alpha-2B adrenergic receptor binding protein binding adrenergic receptor binding signaling receptor binding G protein-coupled receptor binding alpha-2C adrenergic receptor binding alpha-2A adrenergic receptor binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding identical protein binding	cellular response to nitrogen compound cellular response to stimulus response to norepinephrine response to stimulus response to monoamine response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to norepinephrine stimulus cellular response to chemical stimulus cellular response to monoamine stimulus response to catecholamine response to chemical cellular response to catecholamine stimulus cellular response to nitrogen compound cellular response to stimulus response to norepinephrine response to stimulus response to monoamine response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to norepinephrine stimulus cellular response to chemical stimulus cellular response to monoamine stimulus response to catecholamine response to chemical cellular response to catecholamine stimulus cellular process developmental process multicellular organism development multicellular organismal process central nervous system development anatomical structure development nervous system development system development anatomical structure morphogenesis animal organ development animal organ morphogenesis nucleobase-containing compound metabolic process RNA metabolic process metabolic process primary metabolic process macromolecule metabolic process cytosolic mRNA polyadenylation mRNA metabolic process nucleic acid metabolic process localization import into cell transport endocytosis establishment of localization vesicle-mediated transport cellular component organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization apoptotic process cell death programmed cell death regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process protein metabolic process regulation of metabolic process axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation plasma membrane bounded cell projection organization axon development cell morphogenesis involved in neuron differentiation generation of neurons neuron development head development forebrain development brain development cell adhesion signaling negative regulation of signaling negative regulation of biological process regulation of signal transduction negative regulation of G protein-coupled receptor signaling pathway negative regulation of cell communication cell communication negative regulation of cellular process signal transduction regulation of G protein-coupled receptor signaling pathway regulation of signaling negative regulation of response to stimulus adenylate cyclase-activating G protein-coupled receptor signaling pathway negative regulation of signal transduction negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway regulation of response to stimulus adenylate cyclase-modulating G protein-coupled receptor signaling pathway regulation of cell communication G protein-coupled receptor signaling pathway regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway	basement membrane extracellular matrix cellular anatomical structure external encapsulating structure extracellular region cell periphery plasma membrane membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen basement membrane extracellular matrix cellular anatomical structure external encapsulating structure extracellular region cell periphery plasma membrane membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen Golgi apparatus cytoplasm endomembrane system perinuclear region of cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR019744	Amyloidogenic glycoprotein, copper-binding domain conserved site	Conserved Site
A, B	IPR019745	Amyloidogenic glycoprotein, intracellular domain, conserved site	Conserved Site
A, B	IPR011178	Amyloidogenic glycoprotein, copper-binding	Domain
A, B	IPR008154	Amyloidogenic glycoprotein, extracellular	Domain
A, B	IPR015849	Amyloidogenic glycoprotein, heparin-binding	Domain
A, B	IPR019543	Beta-amyloid precursor protein C-terminal	Domain
A, B	IPR036176	E2 domain superfamily	Homologous Superfamily
A, B	IPR036454	Amyloidogenic glycoprotein, heparin-binding domain superfamily	Homologous Superfamily
A, B	IPR024329	Amyloidogenic glycoprotein, E2 domain	Domain
A, B	IPR036669	Amyloidogenic glycoprotein, copper-binding domain superfamily	Homologous Superfamily
A, B	IPR008155	Amyloidogenic glycoprotein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P51693	adenoma gastric carcinoma lung carcinoma malignant mesothelioma nephrotic syndrome osteosarcoma subependymal giant cell astrocytoma astrocytic tumor glioblastoma malignant ependymoma malignant pancreatic neoplasm neurodegenerative disease pancreatic ductal adenocarcinoma atypical teratoid rhabdoid tumor large cell medulloblastoma adenoma gastric carcinoma lung carcinoma malignant mesothelioma nephrotic syndrome osteosarcoma subependymal giant cell astrocytoma astrocytic tumor glioblastoma malignant ependymoma malignant pancreatic neoplasm neurodegenerative disease pancreatic ductal adenocarcinoma atypical teratoid rhabdoid tumor large cell medulloblastoma malignant glioma medulloblastoma oligodendroglioma pilocytic astrocytoma

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.