4RGN | pdb_00004rgn

Structure of Staphylococcal Enterotoxin B bound to two neutralizing antibodies, 14G8 and 6D3

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
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)
J [auth G]	d4rgng1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
J [auth G]	d4rgng2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d4rgne1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d4rgne2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
I [auth F]	d4rgnf1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
I [auth F]	d4rgnf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d4rgnd1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d4rgnd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
H [auth L]	d4rgnl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
H [auth L]	d4rgnl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d4rgnc2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d4rgnc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G [auth H]	d4rgnh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d4rgnb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth S]	d4rgns1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Staphylococcal enterotoxin B, SEB	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
F [auth S]	d4rgns2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Superantigen toxins, C-terminal domain	Superantigen toxins, C-terminal domain	Staphylococcal enterotoxin B, SEB	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d4rgna1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Staphylococcal enterotoxin B, SEB	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d4rgna2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Superantigen toxins, C-terminal domain	Superantigen toxins, C-terminal domain	Staphylococcal enterotoxin B, SEB	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth S]	SCOP2B Superfamily	Superantigen toxins C-terminal domain-like	8034577	3000376	SCOP2B (2022-06-29)
F [auth S]	SCOP2B Superfamily	Bacterial enterotoxins	8041881	3000434	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Superantigen toxins C-terminal domain-like	8034577	3000376	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Bacterial enterotoxins	8041881	3000434	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)
J [auth G]	Cas_Cas5d	e4rgnG1	A: a/b three-layered sandwiches	X: Formyltransferase	H: Formyltransferase	T: Formyltransferase	F: Cas_Cas5d	ECOD (v294.1)
E	Cas_Cas5d	e4rgnE1	A: a/b three-layered sandwiches	X: Formyltransferase	H: Formyltransferase	T: Formyltransferase	F: Cas_Cas5d	ECOD (v294.1)
I [auth F]	Cas_Cas5d	e4rgnF1	A: a/b three-layered sandwiches	X: Formyltransferase	H: Formyltransferase	T: Formyltransferase	F: Cas_Cas5d	ECOD (v294.1)
D	Cas_Cas5d	e4rgnD1	A: a/b three-layered sandwiches	X: Formyltransferase	H: Formyltransferase	T: Formyltransferase	F: Cas_Cas5d	ECOD (v294.1)
H [auth L]	Cas_Cas5d	e4rgnL1	A: a/b three-layered sandwiches	X: Formyltransferase	H: Formyltransferase	T: Formyltransferase	F: Cas_Cas5d	ECOD (v294.1)
C	Cas_Cas5d	e4rgnC1	A: a/b three-layered sandwiches	X: Formyltransferase	H: Formyltransferase	T: Formyltransferase	F: Cas_Cas5d	ECOD (v294.1)
G [auth H]	Cas_Cas5d	e4rgnH1	A: a/b three-layered sandwiches	X: Formyltransferase	H: Formyltransferase	T: Formyltransferase	F: Cas_Cas5d	ECOD (v294.1)
B	Cas_Cas5d	e4rgnB1	A: a/b three-layered sandwiches	X: Formyltransferase	H: Formyltransferase	T: Formyltransferase	F: Cas_Cas5d	ECOD (v294.1)
F [auth S]	Cas_Cas5d	e4rgnS1	A: a/b three-layered sandwiches	X: Formyltransferase	H: Formyltransferase	T: Formyltransferase	F: Cas_Cas5d	ECOD (v294.1)
A	MoCoBD_2	e4rgnA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: MoCoBD_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J [auth G]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I [auth F]	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)
H [auth L]	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)
G [auth H]	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)
F [auth S]	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
F [auth S]	2.40.50.110	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
A	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
A	2.40.50.110	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		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
E, J [auth G]	6D3	L-KAPPA	Mus musculus (house mouse)	IGKV8-1901, IGKJ501, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202613-0)
D, I [auth F]	6D3	VH-CH1	Mus musculus (house mouse)	IGHV1-6902, IGHJ401, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202613-0)
C, H [auth L]	14G8	L-KAPPA	Mus musculus (house mouse)	IGKV5-3901, IGKJ102, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202613-0)
B, G [auth H]	14G8	VH-CH1	Mus musculus (house mouse)	IGHV5S401, IGHJ301, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202613-0)
A, F [auth S]	Superantigen enterotoxin type B (SEB)	Toxin	Staphylococcus aureus	entB*01	R-LIKE-DOMAIN SAG-DOMAIN	TOX	Protein	IMGT (202613-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E, J [auth G]	Light Chain	IGKV8	Kappa	enterotoxin type b	SAbDab (2026-04-10)
D, I [auth F]	Heavy Chain	IGHV1	-	enterotoxin type b	SAbDab (2026-04-10)
C, H [auth L]	Light Chain	IGKV5	Kappa	enterotoxin type b	SAbDab (2026-04-10)
B, G [auth H]	Heavy Chain	IGHV5	-	enterotoxin type b	SAbDab (2026-04-10)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, J [auth G]	6D3 light chain	-	-	-
D, I [auth F]	6D3 heavy chain	-	-	-
C, H [auth L]	14G8 light chain	-	-	-
B, G [auth H]	14G8 heavy chain	-	-	-
A, F [auth S]	Enterotoxin type B	cation binding ion binding binding metal ion binding small molecule binding toxin activity	-	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, F [auth S]	IPR006123	Staphylococcal/Streptococcal toxin, beta-grasp domain	Domain
A, F [auth S]	IPR006177	Staphylococcal/streptococcal toxin, bacterial	Family
A, F [auth S]	IPR006126	Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site	Conserved Site
A, F [auth S]	IPR016091	Superantigen toxin, C-terminal	Homologous Superfamily
A, F [auth S]	IPR006173	Staphylococcal/Streptococcal toxin, OB-fold	Domain
A, F [auth S]	IPR013307	Superantigen, staphylococcal/streptococcal toxin, bacterial	Family
A, F [auth S]	IPR008992	Enterotoxin	Homologous Superfamily

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.