2R56

Crystal Structure of a Recombinant IgE Fab Fragment in Complex with Bovine Beta-Lactoglobulin Allergen

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab 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	d2r56a_	All beta proteins	Lipocalins	Lipocalins	Retinol binding protein-like	beta-Lactoglobulin	cattle (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
D [auth B]	d2r56b_	All beta proteins	Lipocalins	Lipocalins	Retinol binding protein-like	beta-Lactoglobulin	cattle (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
B [auth L]	d2r56l2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d2r56l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth M]	d2r56m2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth M]	d2r56m1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth H]	d2r56h_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth I]	d2r56i_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Lipocalins	8042609	3001332	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Lipocalins	8042609	3001332	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	Lipocalin	e2r56A1	A: beta barrels	X: Lipocalins/Streptavidin	H: Lipocalins (From Topology)	T: Lipocalins	F: Lipocalin	ECOD (1.6)
D [auth B]	Lipocalin	e2r56B1	A: beta barrels	X: Lipocalins/Streptavidin	H: Lipocalins (From Topology)	T: Lipocalins	F: Lipocalin	ECOD (1.6)
B [auth L]	C1-set_4	e2r56L2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B [auth L]	V-set	e2r56L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
E [auth M]	C1-set_4	e2r56M2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
E [auth M]	V-set	e2r56M1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
C [auth H]	C1-set_1	e2r56H2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C [auth H]	V-set_12	e2r56H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
F [auth I]	C1-set_1	e2r56I2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
F [auth I]	V-set_12	e2r56I1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)
D [auth B]	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth I]	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
B [auth L], E [auth M]	IgE Fab Fragment	L-KAPPA	Homo sapiens (human)	IGKV1D-1601, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202506-0)
C [auth H], F [auth I]	IgE Fab Fragment	VH-CH1	Homo sapiens (human)	IGHV3-2301, IGHV3-3018, IGHV3-2304, IGHV3-23D01, IGHJ201, IGHG101, IGHG102, IGHG104	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202506-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L], E [auth M]	Light Chain	IGKV1	Kappa	beta-lactoglobulin	SAbDab (2025-02-21)
C [auth H], F [auth I]	Heavy Chain	IGHV3	-	beta-lactoglobulin	SAbDab (2025-02-21)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth B]	PF00061	Lipocalin / cytosolic fatty-acid binding protein family (Lipocalin)	Lipocalin / cytosolic fatty-acid binding protein family	Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid ...	Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth B]	Beta-lactoglobulin	vitamin binding binding alcohol binding isoprenoid binding retinoid binding lipid binding retinol binding small molecule binding fatty acid binding organic acid binding ion binding anion binding long-chain fatty acid binding carboxylic acid binding vitamin binding binding alcohol binding isoprenoid binding retinoid binding lipid binding retinol binding small molecule binding fatty acid binding organic acid binding ion binding anion binding long-chain fatty acid binding carboxylic acid binding monocarboxylic acid binding identical protein binding protein binding	-	cellular anatomical structure extracellular region
B [auth L], E [auth M]	IgE Fab Fragment, light chain	-	-	-
C [auth H], F [auth I]	IgE Fab Fragment, heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B]	IPR002447	Beta-lactoglobulin	Family
A, D [auth B]	IPR012674	Calycin	Homologous Superfamily
A, D [auth B]	IPR002345	Lipocalin	Family
A, D [auth B]	IPR000566	Lipocalin/cytosolic fatty-acid binding domain	Domain
A, D [auth B]	IPR022272	Lipocalin family conserved site	Conserved Site

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.