4FMF | pdb_00004fmf

Crystal structure of human nectin-1 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)
D	I-set_2	e4fmfD1	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)
D	I-set_8	e4fmfD2	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)
D	V-set_15	e4fmfD3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_15	ECOD (1.6)
C	I-set_2	e4fmfC14	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)
C	I-set_8	e4fmfC15	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)
C	V-set_15	e4fmfC13	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_15	ECOD (1.6)
B	I-set_2	e4fmfB14	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)
B	I-set_8	e4fmfB15	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)
B	V-set_15	e4fmfB13	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_15	ECOD (1.6)
A	I-set_2	e4fmfA4	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	e4fmfA5	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)
A	V-set_15	e4fmfA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_15	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
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, B, C, D	Poliovirus receptor-related protein 1	1V-1C-1C-LIKE	Homo sapiens (human)	PVRL1*01	V-LIKE-DOMAIN V-LIKE, C-LIKE-DOMAIN C-LIKE	RPI	1V-1C-1C-LIKE	IMGT (202542-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13927	Immunoglobulin domain (Ig_3)	Immunoglobulin domain	This family contains immunoglobulin-like domains.	Domain
A, B, C, D	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, B, C, D	Poliovirus receptor-related protein 1	protein binding binding virus receptor activity exogenous protein binding molecular transducer activity coreceptor activity signaling receptor activity cell adhesion molecule binding cell adhesion mediator activity carbohydrate binding identical protein binding protein homodimerization activity protein dimerization activity protein-containing complex binding protein binding binding virus receptor activity exogenous protein binding molecular transducer activity coreceptor activity signaling receptor activity cell adhesion molecule binding cell adhesion mediator activity carbohydrate binding identical protein binding protein homodimerization activity protein dimerization activity protein-containing complex binding virion binding	cellular component organization cell junction organization desmosome organization cellular process cellular component organization or biogenesis cell-cell junction organization localization transport iron ion transport transition metal ion transport monoatomic ion transport monoatomic cation transport establishment of localization metal ion transport cellular component organization cell junction organization desmosome organization cellular process cellular component organization or biogenesis cell-cell junction organization localization transport iron ion transport transition metal ion transport monoatomic ion transport monoatomic cation transport establishment of localization metal ion transport response to stimulus immune response immune system process developmental process enamel mineralization tooth mineralization odontogenesis of dentin-containing tooth odontogenesis animal organ development amelogenesis tissue development anatomical structure morphogenesis anatomical structure development anatomical structure formation involved in morphogenesis animal organ morphogenesis biomineral tissue development multicellular organismal process sensory organ development eye development retina development in camera-type eye visual system development multicellular organism development camera-type eye development sensory system development system development 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 cell adhesion cell-cell adhesion ear morphogenesis embryonic organ morphogenesis ear development embryonic morphogenesis embryo development sensory organ morphogenesis inner ear development cochlea development inner ear morphogenesis cochlea morphogenesis embryonic organ development 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 guidance nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons neuron projection guidance neuron development homophilic cell-cell adhesion macromolecule localization intracellular protein localization protein localization to cell junction camera-type eye morphogenesis eye morphogenesis lens morphogenesis in camera-type eye lens development in camera-type eye regulation of cellular component organization regulation of cellular process cellular component biogenesis cellular component assembly cell junction assembly regulation of synapse structure or activity regulation of synapse assembly synapse organization regulation of biological quality regulation of biological process biological regulation regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization synapse assembly	cellular anatomical structure membrane cell periphery plasma membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection cell-cell junction anchoring junction cell junction cell-cell contact zone cellular anatomical structure membrane cell periphery plasma membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection cell-cell junction anchoring junction cell junction cell-cell contact zone apical junction complex synapse presynaptic active zone membrane presynaptic membrane synaptic membrane presynapse plasma membrane region presynaptic active zone adherens junction neuron to neuron synapse hippocampal mossy fiber to CA3 synapse extracellular region axon growth cone membrane growth cone distal axon site of polarized growth

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR051427	Nectin and Nectin-like	Family
A, B, C, D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR003598	Immunoglobulin subtype 2	Domain
A, B, C, D	IPR013106	Immunoglobulin V-set domain	Domain
A, B, C, D	IPR003599	Immunoglobulin domain subtype	Domain
A, B, C, D	IPR041849	Nectin-1, first immunoglobulin variable domain	Domain
A, B, C, D	IPR041850	Nectin-1, second immunoglobulin domain	Domain
A, B, C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D	IPR013162	CD80-like, immunoglobulin C2-set	Domain
A, B, C, D	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q15223	cleft lip/palate-ectodermal dysplasia syndrome Zlotogora-Ogur syndrome Herpesviridae infectious disease malignant ependymoma Rosselli-Gulienetti syndrome cleft lip and alveolus intellectual disability non-small cell lung carcinoma lung cancer osteosarcoma

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.