6BYV

Solution NMR structure of cysteine-rich calcium bound domains of very low density lipoprotein receptor

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6byva1	Small proteins	LDL receptor-like module	LDL receptor-like module	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)
A	SCOP2B Superfamily	LDL receptor-like module	8035671	3000728	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)
A	PF00057	e6byvA1	A: few secondary structure elements	X: EGF-like	H: LDL receptor-like module (From Topology)	T: LDL receptor-like module	F: PF00057	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00057	Low-density lipoprotein receptor domain class A (Ldl_recept_a)	Low-density lipoprotein receptor domain class A	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Very low-density lipoprotein receptor	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding reelin receptor activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity apolipoprotein binding protein binding lipoprotein particle receptor activity cargo receptor activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding reelin receptor activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity apolipoprotein binding protein binding lipoprotein particle receptor activity cargo receptor activity very-low-density lipoprotein particle receptor activity low-density lipoprotein particle receptor activity lipoprotein particle binding protein-containing complex binding protein-lipid complex binding very-low-density lipoprotein particle binding calcium-dependent protein binding	multicellular organismal process regulation of biological process very-low-density lipoprotein particle clearance plasma lipoprotein particle clearance biological regulation regulation of plasma lipoprotein particle levels localization transport macromolecule localization organic substance transport lipid localization lipid transport establishment of localization protein localization multicellular organismal process regulation of biological process very-low-density lipoprotein particle clearance plasma lipoprotein particle clearance biological regulation regulation of plasma lipoprotein particle levels localization transport macromolecule localization organic substance transport lipid localization lipid transport establishment of localization protein localization establishment of protein localization cellular localization nitrogen compound transport carbohydrate derivative transport protein transport glycoprotein transport cellular macromolecule localization cellular process behavior system process learning or memory nervous system process cognition memory cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis dendrite development cell differentiation anatomical structure development cellular component organization or biogenesis system development developmental process plasma membrane bounded cell projection organization dendrite morphogenesis nervous system development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development organic hydroxy compound metabolic process sterol metabolic process steroid metabolic process cholesterol metabolic process alcohol metabolic process primary metabolic process organic cyclic compound metabolic process secondary alcohol metabolic process organic substance metabolic process small molecule metabolic process metabolic process lipid metabolic process cellular response to stimulus regulation of cellular process response to stimulus signaling signal transduction cell communication spinal cord development central nervous system development ventral spinal cord development cell surface receptor signaling pathway reelin-mediated signaling pathway regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization regulation of developmental process positive regulation of biological process positive regulation of developmental process positive regulation of neuron projection development positive regulation of cell projection organization positive regulation of cellular process regulation of cell projection organization positive regulation of dendrite development regulation of dendrite development regulation of plasma membrane bounded cell projection organization import into cell receptor-mediated endocytosis endocytosis vesicle-mediated transport	clathrin-coated pit membrane cellular anatomical entity endomembrane system cell periphery plasma membrane protein-containing complex receptor complex vacuolar membrane membrane-bounded organelle intracellular anatomical structure lytic vacuole vacuole intracellular membrane-bounded organelle clathrin-coated pit membrane cellular anatomical entity endomembrane system cell periphery plasma membrane protein-containing complex receptor complex vacuolar membrane membrane-bounded organelle intracellular anatomical structure lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cytoplasm organelle membrane lysosome very-low-density lipoprotein particle extracellular region plasma lipoprotein particle extracellular space triglyceride-rich plasma lipoprotein particle lipoprotein particle protein-lipid complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
A	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
A	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
A	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
A	IPR000742	EGF-like domain	Domain
A	IPR000033	LDLR class B repeat	Repeat
A	IPR001881	EGF-like calcium-binding domain	Domain
A	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
A	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P98155	obesity disorder cerebellar ataxia, intellectual disability, and dysequilibrium syndrome 1 intellectual disability malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous neoplasm psoriasis astrocytic tumor ulcerative colitis Autistic Disorder cerebellar ataxia, intellectual disability, and dysequilibrium cerebrovascular disorder invasive ductal breast carcinoma malignant ependymoma medulloblastoma ovarian cancer obesity disorder cerebellar ataxia, intellectual disability, and dysequilibrium syndrome 1 intellectual disability malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous neoplasm psoriasis astrocytic tumor ulcerative colitis Autistic Disorder cerebellar ataxia, intellectual disability, and dysequilibrium cerebrovascular disorder invasive ductal breast carcinoma malignant ependymoma medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia schizophrenia breast carcinoma ductal breast carcinoma in situ esophageal adenocarcinoma large cell medulloblastoma malignant mesothelioma myopathy pancreatic intraductal papillary-mucinous carcinoma Pick disease spina bifida autism breast fibroadenoma lung cancer

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 R01GM133198.