3W2D | pdb_00003w2d

Crystal Structure of Staphylococcal Eenterotoxin B in complex with a novel neutralization monoclonal antibody Fab fragment

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)
B [auth L]	d3w2dl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth L]	d3w2dl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3w2da1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Staphylococcal enterotoxin B, SEB	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d3w2da2	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)
C [auth H]	d3w2dh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth L]	C1-set_4	e3w2dL1	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	e3w2dL2	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)
A	Stap_Strp_toxin	e3w2dA1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: Stap_Strp_toxin	ECOD (1.6)
A	Stap_Strp_tox_C	e3w2dA2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Stap_Strp_tox_C	ECOD (1.6)
C [auth H]	V-set_8	e3w2dH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C [auth H]	C1-set_1	e3w2dH1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	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)
C [auth H]	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]	3E2 Fab	L-KAPPA	Mus musculus (house mouse)	IGKV4-57-101, IGKJ101, IGKJ201, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202537-0)
A	Superantigen enterotoxin type B (SEB)	Toxin	Staphylococcus aureus	entB*01	R-LIKE-DOMAIN SAG-DOMAIN	TOX	Protein	IMGT (202537-0)
C [auth H]	3E2 Fab	VH-CH1	Mus musculus (house mouse)	IGHV3-202, IGHJ301, IGHG1*01	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202537-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L]	Light Chain	IGKV4	Kappa	enterotoxin type b	SAbDab (2025-09-26)
C [auth H]	Heavy Chain	IGHV3	-	enterotoxin type b	SAbDab (2025-09-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01123	Staphylococcal/Streptococcal toxin, OB-fold domain (Stap_Strp_toxin)	Staphylococcal/Streptococcal toxin, OB-fold domain	This entry represents an OB-fold domain found in enterotoxins.	Domain
A	PF02876	Staphylococcal/Streptococcal toxin, beta-grasp domain (Stap_Strp_tox_C)	Staphylococcal/Streptococcal toxin, beta-grasp domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth L]	Monoclonal Antibody 3E2 Fab figment light chain	-	-	-
A	Enterotoxin type B	cation binding ion binding binding metal ion binding small molecule binding toxin activity	-	cellular anatomical structure extracellular region
C [auth H]	Monoclonal Antibody 3E2 Fab figment heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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