5ZO2

Crystal structure of mouse nectin-like molecule 4 (mNecl-4) full ectodomain in complex with mouse nectin-like molecule 1 (mNecl-1) Ig1 domain, 3.3A

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	I-set_2	e5zo2A2	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	e5zo2A1	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 [auth C]	I-set_6	e5zo2C3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_6	ECOD (1.6)
B [auth C]	I-set_2	e5zo2C2	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 [auth C]	I-set_8	e5zo2C1	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 [auth B]	I-set_6	e5zo2B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_6	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth B]	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 [auth C]	CADM4 (Cell adhesion molecule 4)	1V-1C-1C-LIKE	Mus musculus (house mouse)	CADM4*01	V-LIKE-DOMAIN V-LIKE, C-LIKE-DOMAIN C-LIKE	RPI	1V-1C-1C-LIKE	IMGT (202507-0)
C [auth B]	CADM3 (Cell adhesion molecule 3)	1V-LIKE	Mus musculus (house mouse)	CADM3*01	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE	IMGT (202507-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C]	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, B [auth C]	PF13927	Immunoglobulin domain (Ig_3)	Immunoglobulin domain	This family contains immunoglobulin-like domains.	Domain
A, B [auth C]	PF08205	CD80-like C2-set immunoglobulin domain (C2-set_2)	CD80-like C2-set immunoglobulin domain	These domains belong to the immunoglobulin superfamily.	Domain
C [auth B]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C]	Cell adhesion molecule 4	vascular endothelial growth factor receptor 1 binding protein binding binding signaling receptor binding cytokine receptor binding vascular endothelial growth factor receptor binding growth factor receptor binding protein phosphatase binding phosphatase binding enzyme binding vascular endothelial growth factor receptor 2 binding protein tyrosine kinase binding kinase binding receptor tyrosine kinase binding vascular endothelial growth factor receptor 1 binding protein binding binding signaling receptor binding cytokine receptor binding vascular endothelial growth factor receptor binding growth factor receptor binding protein phosphatase binding phosphatase binding enzyme binding vascular endothelial growth factor receptor 2 binding protein tyrosine kinase binding kinase binding receptor tyrosine kinase binding protein kinase binding	cellular response to stimulus regulation of biological process regulation of signaling small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling regulation of small GTPase mediated signal transduction Rac protein signal transduction biological regulation regulation of signal transduction intracellular signal transduction regulation of Rac protein signal transduction cell communication regulation of intracellular signal transduction cellular response to stimulus regulation of biological process regulation of signaling small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling regulation of small GTPase mediated signal transduction Rac protein signal transduction biological regulation regulation of signal transduction intracellular signal transduction regulation of Rac protein signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette regulation of cell communication cellular process signal transduction regulation of protein modification process regulation of protein phosphorylation negative regulation of biological process regulation of peptidyl-threonine phosphorylation negative regulation of phosphate metabolic process regulation of primary metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process negative regulation of cellular process peptidyl-amino acid modification protein metabolic process peptidyl-threonine modification protein modification process phosphorus metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process negative regulation of protein phosphorylation macromolecule modification negative regulation of peptidyl-threonine phosphorylation negative regulation of phosphorus metabolic process metabolic process regulation of phosphorylation regulation of phosphorus metabolic process macromolecule metabolic process negative regulation of phosphorylation regulation of metabolic process peptidyl-threonine phosphorylation cellular component organization cell adhesion cell junction organization cell-cell adhesion synaptic membrane adhesion synapse organization cellular component organization or biogenesis cell-cell adhesion via plasma-membrane adhesion molecules peptidyl-tyrosine modification negative regulation of peptidyl-tyrosine phosphorylation regulation of peptidyl-tyrosine phosphorylation peptidyl-tyrosine phosphorylation cellular response to growth factor stimulus negative regulation of signaling negative regulation of cellular response to growth factor stimulus cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication regulation of vascular endothelial growth factor receptor signaling pathway cellular response to endogenous stimulus negative regulation of vascular endothelial growth factor receptor signaling pathway enzyme-linked receptor protein signaling pathway cell surface receptor signaling pathway negative regulation of response to stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus negative regulation of signal transduction vascular endothelial growth factor receptor signaling pathway response to growth factor wound healing response to stress regulation of response to stress regulation of wound healing response to wounding regulation of response to wounding negative regulation of vascular endothelial growth factor signaling pathway regulation of vascular endothelial growth factor signaling pathway regulation of cellular response to vascular endothelial growth factor stimulus vascular endothelial growth factor signaling pathway cellular response to vascular endothelial growth factor stimulus negative regulation of cellular response to vascular endothelial growth factor stimulus cell population proliferation regulation of cell population proliferation regulation of cell motility regulation of locomotion cell motility locomotion	cell periphery cellular anatomical structure membrane plasma membrane synapse cell junction plasma membrane region synaptic membrane cell leading edge cell-cell junction anchoring junction cell-cell contact zone
C [auth B]	Cell adhesion molecule 3	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity	protein localization localization cellular localization cellular macromolecule localization macromolecule localization cellular process cell adhesion cell-cell adhesion cell-cell adhesion via plasma-membrane adhesion molecules homophilic cell adhesion via plasma membrane adhesion molecules heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules	cell-cell junction cellular anatomical structure anchoring junction cell junction parallel fiber to Purkinje cell synapse synapse excitatory synapse cell periphery presynapse membrane plasma membrane presynaptic membrane plasma membrane region synaptic membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B [auth C]	IPR003598	Immunoglobulin subtype 2	Domain
A, B [auth C]	IPR013106	Immunoglobulin V-set domain	Domain
A, B [auth C]	IPR003599	Immunoglobulin domain subtype	Domain
A, B [auth C]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B [auth C]	IPR013162	CD80-like, immunoglobulin C2-set	Domain
A, B [auth C]	IPR007110	Immunoglobulin-like domain	Domain
A, B [auth C]	IPR003585	Neurexin/syndecan/glycophorin C	Domain
C [auth B]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth B]	IPR003598	Immunoglobulin subtype 2	Domain
C [auth B]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth B]	IPR013106	Immunoglobulin V-set domain	Domain
C [auth B]	IPR003599	Immunoglobulin domain subtype	Domain
C [auth B]	IPR013162	CD80-like, immunoglobulin C2-set	Domain
C [auth B]	IPR007110	Immunoglobulin-like domain	Domain
C [auth B]	IPR003585	Neurexin/syndecan/glycophorin C	Domain

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.