4FOM | pdb_00004fom

Crystal structure of human nectin-3 full ectodomain (D1-D3)

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	V-set_9	e4fomA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_9	ECOD (1.6)
A	I-set_2	e4fomA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_2	ECOD (1.6)
A	I-set_8	e4fomA3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_8	ECOD (1.6)

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)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A	Poliovirus receptor-related protein 3	1V-1C-1C-LIKE	Homo sapiens (human)	PVRL3*01	V-LIKE-DOMAIN V-LIKE, C-LIKE-DOMAIN C-LIKE	RPI	1V-1C-1C-LIKE	IMGT (202537-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
A	PF08205	CD80-like C2-set immunoglobulin domain (C2-set_2)	CD80-like C2-set immunoglobulin domain	These domains belong to the immunoglobulin superfamily.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Poliovirus receptor-related protein 3	cell adhesion molecule binding protein binding binding cell adhesion mediator activity identical protein binding protein homodimerization activity protein dimerization activity	sexual reproduction reproductive process fertilization biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules cell adhesion cell-cell adhesion cellular process sexual reproduction reproductive process fertilization biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules cell adhesion cell-cell adhesion cellular process cell-cell adhesion via plasma-membrane adhesion molecules multicellular organismal process regulation of cellular component organization regulation of cellular process cellular component organization cellular component biogenesis multicellular organism development cellular component assembly regulation of postsynapse assembly cell junction assembly anatomical structure development regulation of synapse structure or activity synapse organization cellular component organization or biogenesis regulation of synapse assembly regulation of biological quality system development developmental process regulation of biological process postsynapse organization postsynapse assembly biological regulation regulation of postsynapse organization nervous system development regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly ear morphogenesis embryonic organ morphogenesis ear development sensory organ development animal organ development embryonic morphogenesis embryo development anatomical structure morphogenesis sensory organ morphogenesis inner ear development cochlea development inner ear morphogenesis cochlea morphogenesis animal organ morphogenesis embryonic organ development camera-type eye morphogenesis eye development visual system development retina development in camera-type eye retina morphogenesis in camera-type eye eye morphogenesis camera-type eye development sensory system development localization establishment of protein localization cellular localization establishment of protein localization to membrane establishment of protein localization to plasma membrane localization within membrane establishment of localization homophilic cell adhesion via plasma membrane adhesion molecules macromolecule localization intracellular protein localization protein localization to cell junction lens morphogenesis in camera-type eye lens development in camera-type eye	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 cell-cell junction anchoring junction somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection cell-cell contact zone apical junction complex adherens junction hippocampal mossy fiber to CA3 synapse axon

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR051427	Nectin and Nectin-like	Family
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A	IPR033319	Nectin-3, immunoglobulin variable domain 1	Domain
A	IPR013106	Immunoglobulin V-set domain	Domain
A	IPR003599	Immunoglobulin domain subtype	Domain
A	IPR033320	Nectin-3/4, second Ig domain	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR013162	CD80-like, immunoglobulin C2-set	Domain
A	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9NQS3	adrenal cortex carcinoma ductal breast carcinoma in situ interstitial cystitis lung adenocarcinoma pituitary cancer atypical teratoid rhabdoid tumor esophageal adenocarcinoma invasive ductal breast carcinoma lung cancer tuberculosis cataract glioblastoma large cell medulloblastoma medulloblastoma ulcerative colitis

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.