5TPT | pdb_00005tpt

The Crystal Structure of Amyloid Precursor-Like Protein 2 (APLP2) E2 Domain

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)
B	d5tptb_	All alpha proteins	STAT-like	CAPPD, an extracellular domain of amyloid beta A4 protein	CAPPD, an extracellular domain of amyloid beta A4 protein	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5tpta_	All alpha proteins	STAT-like	CAPPD, an extracellular domain of amyloid beta A4 protein	CAPPD, an extracellular domain of amyloid beta A4 protein	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	8072397	3001286	SCOP2B (2022-06-29)
A	SCOP2 Family	CAPPD, an extracellular domain of amyloid beta A4 protein	8072396	4002465	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	CAPPD-like	8072397	3001286	SCOP2 (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	APP_E2	e5tptB1	A: alpha bundles	X: STAT-like	H: CAPPD, an extracellular domain of amyloid beta A4 protein (From Topology)	T: CAPPD, an extracellular domain of amyloid beta A4 protein	F: APP_E2	ECOD (1.6)
A	APP_E2	e5tptA1	A: alpha bundles	X: STAT-like	H: CAPPD, an extracellular domain of amyloid beta A4 protein (From Topology)	T: CAPPD, an extracellular domain of amyloid beta A4 protein	F: APP_E2	ECOD (1.6)

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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF12925	E2 domain of amyloid precursor protein (APP_E2)	E2 domain of amyloid precursor protein	The E2 domain is the largest of the conserved domains of the amyloid precursor protein. The structure of E2 consists of two coiled-coil sub-structures connected through a continuous helix, and bears an unexpected resemblance to the spectrin family of ...	The E2 domain is the largest of the conserved domains of the amyloid precursor protein. The structure of E2 consists of two coiled-coil sub-structures connected through a continuous helix, and bears an unexpected resemblance to the spectrin family of protein structures.E 2 can reversibly dimerise in solution, and the dimerisation occurs along the longest dimension of the molecule in an antiparallel orientation, which enables the N-terminal substructure of one monomer to pack against the C-terminal substructure of a second monomer. The high degree of conservation of residues at the putative dimer interface suggests that the E2 dimer observed in the crystal could be physiologically relevant. Heparin sulfate proteoglycans, the putative ligands for the precursor present in extracellular matrix, bind to E2 at a conserved and positively charged site near the dimer interface [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Amyloid-like protein 2	cation binding transition metal ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding enzyme regulator activity molecular function inhibitor activity peptidase regulator activity serine-type endopeptidase inhibitor activity molecular function regulator activity enzyme inhibitor activity cation binding transition metal ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding enzyme regulator activity molecular function inhibitor activity peptidase regulator activity serine-type endopeptidase inhibitor activity molecular function regulator activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding identical protein binding protein binding	developmental process multicellular organism development multicellular organismal process central nervous system development anatomical structure development nervous system development system development axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis developmental process multicellular organism development multicellular organismal process central nervous system development anatomical structure development nervous system development system development axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation cellular component organization or biogenesis plasma membrane bounded cell projection organization axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development cellular process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation G protein-coupled receptor signaling pathway signal transduction cell communication	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane intracellular anatomical structure cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane intracellular anatomical structure platelet alpha granule membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle secretory granule secretory vesicle cytoplasm organelle membrane platelet alpha granule secretory granule membrane membrane-enclosed lumen intracellular organelle lumen endoplasmic reticulum lumen organelle lumen endoplasmic reticulum nucleus

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	IPR002223	Pancreatic trypsin inhibitor Kunitz domain	Domain
A, B	IPR008154	Amyloidogenic glycoprotein, extracellular	Domain
A, B	IPR015849	Amyloidogenic glycoprotein, heparin-binding	Domain
A, B	IPR011993	PH-like domain superfamily	Homologous Superfamily
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	IPR020901	Proteinase inhibitor I2, Kunitz, conserved site	Conserved Site
A, B	IPR036880	Pancreatic trypsin inhibitor Kunitz 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: Q06481	Nerve Degeneration pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia astrocytic tumor Duchenne muscular dystrophy gastric carcinoma lung cancer medulloblastoma pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma coronary artery disease Emery-Dreifuss muscular dystrophy large cell medulloblastoma lymphoplasmacytic lymphoma myocardial ischemia ovarian cancer Nerve Degeneration pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia astrocytic tumor Duchenne muscular dystrophy gastric carcinoma lung cancer medulloblastoma pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma coronary artery disease Emery-Dreifuss muscular dystrophy large cell medulloblastoma lymphoplasmacytic lymphoma myocardial ischemia ovarian cancer pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis cystic fibrosis gastric cancer lung adenocarcinoma malignant pancreatic neoplasm myopathy pancreatic ductal adenocarcinoma

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.