1WGO | pdb_00001wgo

Solution structure of the PKD domain from human VPS10 domain-containing receptor SorCS2

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)
A	d1wgoa1	All beta proteins	Immunoglobulin-like beta-sandwich	PKD domain	PKD domain	VPS10 domain-containing receptor SorCS2	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1wgoa3	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1wgoa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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	SCOP2 Family	PKD domain	8055206	4007526	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PKD domain	8055207	3002045	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)
A	PKD	e1wgoA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PKD	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00801	PKD domain (PKD)	PKD domain	This domain was first identified in the Polycystic kidney disease protein PKD1. This domain has been predicted to contain an Ig-like fold [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	VPS10 domain-containing receptor SorCS2	peptide receptor activity molecular transducer activity G protein-coupled receptor activity G protein-coupled peptide receptor activity signaling receptor activity transmembrane signaling receptor activity neuropeptide receptor activity	cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell communication G protein-coupled receptor signaling pathway cellular process signal transduction neuropeptide signaling pathway cellular localization establishment of protein localization transport cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell communication G protein-coupled receptor signaling pathway cellular process signal transduction neuropeptide signaling pathway cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization intracellular protein localization intracellular protein transport negative regulation of signaling modulation of chemical synaptic transmission negative regulation of biological process negative regulation of synaptic transmission negative regulation of cell communication synaptic signaling negative regulation of cellular process regulation of biological quality regulation of synaptic plasticity trans-synaptic signaling regulation of signaling cell-cell signaling chemical synaptic transmission regulation of trans-synaptic signaling long-term synaptic depression anterograde trans-synaptic signaling regulation of cell communication	postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region somatodendritic compartment cell body perikaryon neuronal cell body endosome membrane membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle recycling endosome endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle recycling endosome membrane vesicle membrane cytoplasmic vesicle cytoplasm vesicle organelle membrane early endosome early endosome membrane neuron spine neuron projection dendritic spine plasma membrane bounded cell projection cell projection dendrite dendritic tree cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR022409	PKD/Chitinase domain	Domain
A	IPR000601	PKD domain	Domain
A	IPR031777	Sortilin, C-terminal	Domain
A	IPR006581	VPS10	Domain
A	IPR050310	VPS10-related sortilin family receptors	Family
A	IPR035986	PKD domain superfamily	Homologous Superfamily
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR031778	Sortilin, N-terminal	Domain
A	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	: Q96PQ0	bipolar disorder malignant glioma subependymal giant cell astrocytoma drug dependence medulloblastoma glioblastoma pilocytic astrocytoma

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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.