4HZA | pdb_00004hza

Crystal Structure of the Immunoglobulin variable domain of Nectin-2 in monoclinic form

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4hzaa1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4hzaa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4hzab1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4hzab2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	p450	e4hzaA1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: p450	ECOD (v294.1)
B	ABC_tran	e4hzaB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (v294.1)

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)
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	Poliovirus receptor-related protein 2	1V-LIKE	Homo sapiens (human)	PVRL2*01	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE	IMGT (202613-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, 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	Poliovirus receptor-related protein 2	protein binding binding virus receptor activity exogenous protein binding molecular transducer activity coreceptor activity signaling receptor activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity cell adhesion molecule binding identical protein binding protein binding binding virus receptor activity exogenous protein binding molecular transducer activity coreceptor activity signaling receptor activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity cell adhesion molecule binding identical protein binding protein homodimerization activity protein dimerization activity	regulation of immune effector process lymphocyte mediated immunity positive regulation of leukocyte mediated immunity positive regulation of response to biotic stimulus regulation of cellular process response to stimulus response to biotic stimulus positive regulation of leukocyte mediated cytotoxicity positive regulation of immune response positive regulation of natural killer cell mediated immunity leukocyte mediated immunity regulation of immune system process natural killer cell mediated immunity positive regulation of immune system process regulation of immune effector process lymphocyte mediated immunity positive regulation of leukocyte mediated immunity positive regulation of response to biotic stimulus regulation of cellular process response to stimulus response to biotic stimulus positive regulation of leukocyte mediated cytotoxicity positive regulation of immune response positive regulation of natural killer cell mediated immunity leukocyte mediated immunity regulation of immune system process natural killer cell mediated immunity positive regulation of immune system process regulation of biological process regulation of natural killer cell mediated immunity immune response response to other organism regulation of innate immune response response to external stimulus leukocyte mediated cytotoxicity immune effector process regulation of leukocyte mediated immunity regulation of response to stimulus defense response to other organism positive regulation of defense response natural killer cell mediated cytotoxicity regulation of immune response positive regulation of natural killer cell mediated cytotoxicity regulation of cell killing positive regulation of cell killing regulation of defense response regulation of response to biotic stimulus regulation of natural killer cell mediated cytotoxicity biological process involved in interspecies interaction between organisms regulation of response to external stimulus positive regulation of lymphocyte mediated immunity positive regulation of biological process positive regulation of response to stimulus positive regulation of response to external stimulus regulation of response to stress response to stress innate immune response positive regulation of immune effector process response to external biotic stimulus positive regulation of cellular process positive regulation of innate immune response defense response regulation of leukocyte mediated cytotoxicity biological regulation defense response to symbiont regulation of lymphocyte mediated immunity immune system process cellular process cell killing adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains T cell mediated immunity positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of adaptive immune response susceptibility to T cell mediated cytotoxicity regulation of T cell mediated immunity T cell mediated cytotoxicity positive regulation of T cell mediated cytotoxicity regulation of adaptive immune response adaptive immune response regulation of T cell mediated cytotoxicity positive regulation of T cell mediated immunity developmental process spermatid development spermatid differentiation sexual reproduction cellular developmental process spermatogenesis reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation male gamete generation cellular component organization nucleus organization organelle organization cell differentiation anatomical structure development germ cell development cellular component organization or biogenesis spermatid nucleus differentiation fertilization sperm mitochondrion organization mitochondrion organization virion attachment to host cell adhesion of symbiont to host cell viral process coreceptor-mediated virion attachment to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction localization cellular localization establishment of localization in cell establishment of localization negative regulation of biological process negative regulation of lymphocyte mediated immunity negative regulation of natural killer cell mediated immunity negative regulation of immune response negative regulation of immune effector process negative regulation of response to external stimulus negative regulation of defense response negative regulation of natural killer cell mediated cytotoxicity negative regulation of response to biotic stimulus negative regulation of leukocyte mediated cytotoxicity negative regulation of cellular process negative regulation of cell killing negative regulation of response to stimulus negative regulation of immune system process negative regulation of leukocyte mediated immunity negative regulation of innate immune response cellular response to stimulus positive regulation of cell communication immune response-regulating cell surface receptor signaling pathway positive regulation of signal transduction positive regulation of T cell receptor signaling pathway signaling regulation of antigen receptor-mediated signaling pathway regulation of signal transduction cell communication immune response-activating signaling pathway immune response-regulating signaling pathway signal transduction regulation of signaling cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway regulation of T cell receptor signaling pathway T cell receptor signaling pathway regulation of cell communication antigen receptor-mediated signaling pathway activation of immune response positive regulation of antigen receptor-mediated signaling pathway positive regulation of signaling cytoskeleton organization membrane organization membrane fusion fusion of virus membrane with host plasma membrane membrane fusion involved in viral entry into host cell positive regulation of B cell mediated immunity regulation of immunoglobulin mediated immune response positive regulation of immunoglobulin mediated immune response regulation of B cell mediated immunity immunoglobulin mediated immune response B cell mediated immunity multicellular organismal process positive regulation of mast cell activation regulation of leukocyte activation cell activation regulation of cell activation myeloid leukocyte activation leukocyte activation positive regulation of cell activation positive regulation of leukocyte activation mast cell activation positive regulation of multicellular organismal process regulation of mast cell activation regulation of multicellular organismal process plasma membrane bounded cell projection organization cell projection organization cilium organization cell adhesion cell-cell adhesion homophilic cell-cell adhesion positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target immune response to tumor cell regulation of natural killer cell mediated cytotoxicity directed against tumor cell target regulation of natural killer cell mediated immune response to tumor cell positive regulation of immune response to tumor cell natural killer cell mediated immune response to tumor cell positive regulation of response to tumor cell positive regulation of natural killer cell mediated immune response to tumor cell regulation of response to tumor cell response to tumor cell regulation of immune response to tumor cell natural killer cell mediated cytotoxicity directed against tumor cell target susceptibility to natural killer cell mediated cytotoxicity cellular component assembly involved in morphogenesis cellular component biogenesis vesicle organization cellular anatomical entity morphogenesis cellular component assembly endomembrane system organization organelle assembly secretory granule organization anatomical structure morphogenesis anatomical structure formation involved in morphogenesis acrosome assembly establishment of organelle localization mitochondrion localization organelle localization establishment of mitochondrion localization modulation by symbiont of entry into host regulation of viral entry into host cell regulation of viral life cycle regulation of viral process symbiont entry into host cell symbiont entry into host regulation of biological process involved in symbiotic interaction	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction membrane cell-cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction membrane cell-cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle cell surface cell periphery plasma membrane apical junction complex adherens junction zonula adherens cell-cell contact zone

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B	IPR013106	Immunoglobulin V-set domain	Domain
A, B	IPR003599	Immunoglobulin domain subtype	Domain
A, B	IPR052659	Nectin and Poliovirus Receptor	Family
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR013162	CD80-like, immunoglobulin C2-set	Domain
A, B	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q92692	Liver Cirrhosis, Experimental vascular dementia abdominal aortic aneurysm atypical teratoid rhabdoid tumor ductal breast carcinoma in situ heart disease metabolic syndrome X osteosarcoma wet macular degeneration age-related macular degeneration breast carcinoma frontotemporal dementia invasive ductal breast carcinoma malignant ependymoma myocardial infarction Liver Cirrhosis, Experimental vascular dementia abdominal aortic aneurysm atypical teratoid rhabdoid tumor ductal breast carcinoma in situ heart disease metabolic syndrome X osteosarcoma wet macular degeneration age-related macular degeneration breast carcinoma frontotemporal dementia invasive ductal breast carcinoma malignant ependymoma myocardial infarction pilocytic astrocytoma Alzheimer disease cerebrovascular disorder glioblastoma Lewy body dementia malignant glioma non-alcoholic fatty liver disease

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.