2YWY | pdb_00002ywy

Structure of new antigen receptor variable domain from sharks

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2ywya_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	spotted wobbegong (Orectolobus maculatus ) [TaxId: 168098 ],	SCOPe (2.08)
C	d2ywyc_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	spotted wobbegong (Orectolobus maculatus ) [TaxId: 168098 ],	SCOPe (2.08)
D	d2ywyd_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	spotted wobbegong (Orectolobus maculatus ) [TaxId: 168098 ],	SCOPe (2.08)
B	d2ywyb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	spotted wobbegong (Orectolobus maculatus ) [TaxId: 168098 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	V set domains-like	8084178	4007530	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Immunoglobulin (Ig) domain-like	8084179	3000071	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8084179	3000071	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8084179	3000071	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8084179	3000071	SCOP2B (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	Rpf1_C	e2ywyA1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Rpf1_C	ECOD (develop294)
C	Rpf1_C	e2ywyC1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Rpf1_C	ECOD (develop294)
D	Rpf1_C	e2ywyD1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Rpf1_C	ECOD (develop294)
B	Rpf1_C	e2ywyB1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Rpf1_C	ECOD (develop294)

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)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	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, C, D	VH from Ig-Heavy-Nu (IgN), New Antigen Receptor (NAR)	VH	Orectolobus maculatus (spotted wobbegong)	IGHV2S5*01, IGHJ5, IGHJ6	V-DOMAIN VH	IG	(VH)	IMGT (202610-0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	new antigen receptor variable domain	binding antigen binding peptide antigen binding peptide binding	response to stimulus immune response immune system process adaptive immune response	cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex T cell receptor complex receptor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR051006	T cell receptor variable domain	Family
A, B, C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR013106	Immunoglobulin V-set domain	Domain
A, B, C, D	IPR003599	Immunoglobulin domain subtype	Domain
A, B, C, D	IPR007110	Immunoglobulin-like domain	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.