2I25

Crystal structure analysis of the nurse shark New antigen Receptor PBLA8 variable domain in complex with lysozyme

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
Protein Family 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 [auth N]	d2i25n1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	nurse shark (Ginglymostoma cirratum ) [TaxId: 7801 ],	SCOPe (2.08)
A [auth N]	d2i25n2	Artifacts	Tags	Tags	Tags	C-terminal Tags	nurse shark (Ginglymostoma cirratum ) [TaxId: 7801 ],	SCOPe (2.08)
C [auth O]	d2i25o1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	nurse shark (Ginglymostoma cirratum ) [TaxId: 7801 ],	SCOPe (2.08)
C [auth O]	d2i25o2	Artifacts	Tags	Tags	Tags	C-terminal Tags	nurse shark (Ginglymostoma cirratum ) [TaxId: 7801 ],	SCOPe (2.08)
B [auth L]	d2i25l_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	C-type lysozyme	Lysozyme	(Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)
D [auth M]	d2i25m_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	C-type lysozyme	Lysozyme	(Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth N]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8086010	3000071	SCOP2B (2022-06-29)
C [auth O]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8086010	3000071	SCOP2B (2022-06-29)
B [auth L]	SCOP2B Superfamily	Lysozyme-like	8037428	3001879	SCOP2B (2022-06-29)
D [auth M]	SCOP2B Superfamily	Lysozyme-like	8037428	3001879	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 [auth N]	Beta-APP	e2i25N1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Beta-APP	ECOD (1.6)
C [auth O]	Beta-APP	e2i25O1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Beta-APP	ECOD (1.6)
B [auth L]	Lys	e2i25L1	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Lys	ECOD (1.6)
D [auth M]	Lys	e2i25M1	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Lys	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth N]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth O]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth L]	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)
D [auth M]	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		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 [auth N], C [auth O]	VH IGHN (IgNAR) PBLA8, anti-lysozyme C [hen egg white]	VH	Ginglymostoma cirratum (nurse shark)	IGHV2S5101, IGHJ101	V-DOMAIN VH	IG	(VH)	IMGT (202450-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth N], C [auth O]	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
B [auth L], D [auth M]	PF00062	C-type lysozyme/alpha-lactalbumin family (Lys)	C-type lysozyme/alpha-lactalbumin family	Alpha-lactalbumin is the regulatory subunit of lactose synthase, changing the substrate specificity of galactosyltransferase from N-acetylglucosamine to glucose. C-type lysozymes are secreted bacteriolytic enzymes that cleave the peptidoglycan of bac ...	Alpha-lactalbumin is the regulatory subunit of lactose synthase, changing the substrate specificity of galactosyltransferase from N-acetylglucosamine to glucose. C-type lysozymes are secreted bacteriolytic enzymes that cleave the peptidoglycan of bacterial cell walls. Structure is a multi-domain, mixed alpha and beta fold, containing four conserved disulfide bonds.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth N], C [auth O]	New Antigen Receptor PBLA8	binding antigen binding peptide antigen binding peptide binding	-	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
B [auth L], D [auth M]	Lysozyme C	hydrolase activity, acting on glycosyl bonds hexosaminidase activity beta-N-acetylhexosaminidase activity beta-N-acetylglucosaminidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity peptidoglycan muralytic activity lysozyme activity identical protein binding protein binding binding	catabolic process cell wall organization or biogenesis metabolic process cellular process macromolecule metabolic process macromolecule catabolic process cell wall macromolecule catabolic process cell wall macromolecule metabolic process biological process involved in interspecies interaction between organisms disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing response to stimulus catabolic process cell wall organization or biogenesis metabolic process cellular process macromolecule metabolic process macromolecule catabolic process cell wall macromolecule catabolic process cell wall macromolecule metabolic process biological process involved in interspecies interaction between organisms disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing response to stimulus response to other organism defense response response to external stimulus defense response to Gram-negative bacterium response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus defense response to Gram-positive bacterium	cellular anatomical structure intracellular anatomical structure cytoplasm extracellular region extracellular space membrane-bounded organelle intracellular organelle organelle endoplasmic reticulum intracellular membrane-bounded organelle endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth N], C [auth O]	IPR051006	T cell receptor variable domain	Family
A [auth N], C [auth O]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth N], C [auth O]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth N], C [auth O]	IPR013106	Immunoglobulin V-set domain	Domain
A [auth N], C [auth O]	IPR003599	Immunoglobulin domain subtype	Domain
A [auth N], C [auth O]	IPR007110	Immunoglobulin-like domain	Domain
B [auth L], D [auth M]	IPR001916	Glycoside hydrolase, family 22	Family
B [auth L], D [auth M]	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily
B [auth L], D [auth M]	IPR019799	Glycoside hydrolase family 22 domain	Domain
B [auth L], D [auth M]	IPR000974	Glycoside hydrolase, family 22, lysozyme	Family

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.