3R8B | pdb_00003r8b

Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8

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)
P	d3r8bp_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
N	d3r8bn_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
L	d3r8bl_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
J	d3r8bj_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
H	d3r8bh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
F	d3r8bf_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D	d3r8bd_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d3r8bb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
O	d3r8bo1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Staphylococcal enterotoxin B, SEB	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
O	d3r8bo2	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)
M	d3r8bm1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Staphylococcal enterotoxin B, SEB	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
M	d3r8bm2	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)
K	d3r8bk1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Staphylococcal enterotoxin B, SEB	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
K	d3r8bk2	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)
I	d3r8bi1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Staphylococcal enterotoxin B, SEB	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
I	d3r8bi2	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)
G	d3r8bg1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Staphylococcal enterotoxin B, SEB	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
G	d3r8bg2	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)
E	d3r8be1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Staphylococcal enterotoxin B, SEB	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
E	d3r8be2	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	d3r8bc1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Staphylococcal enterotoxin B, SEB	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
C	d3r8bc2	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	d3r8ba1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Staphylococcal enterotoxin B, SEB	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d3r8ba2	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)
O	SCOP2B Superfamily	Bacterial enterotoxins	8041881	3000434	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Superantigen toxins C-terminal domain-like	8034577	3000376	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Superantigen toxins C-terminal domain-like	8034577	3000376	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Bacterial enterotoxins	8041881	3000434	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Bacterial enterotoxins	8041881	3000434	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Superantigen toxins C-terminal domain-like	8034577	3000376	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Superantigen toxins C-terminal domain-like	8034577	3000376	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Bacterial enterotoxins	8041881	3000434	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Bacterial enterotoxins	8041881	3000434	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Superantigen toxins C-terminal domain-like	8034577	3000376	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Superantigen toxins C-terminal domain-like	8034577	3000376	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Bacterial enterotoxins	8041881	3000434	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Superantigen toxins C-terminal domain-like	8034577	3000376	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Bacterial enterotoxins	8041881	3000434	SCOP2B (2022-06-29)
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)
P	Globin	e3r8bP1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Globin	ECOD (v294.1)
N	Globin	e3r8bN1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Globin	ECOD (v294.1)
L	Globin	e3r8bL1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Globin	ECOD (v294.1)
J	Globin	e3r8bJ1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Globin	ECOD (v294.1)
H	Globin	e3r8bH1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Globin	ECOD (v294.1)
F	Globin	e3r8bF1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Globin	ECOD (v294.1)
D	Globin	e3r8bD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Globin	ECOD (v294.1)
B	PPV_E2_C	e3r8bB1	A: a/b three-layered sandwiches	X: N-terminal beta-sandwich domain in anthrax protective antigen	H: N-terminal beta-sandwich domain in anthrax protective antigen	T: N-terminal beta-sandwich domain in anthrax protective antigen	F: PPV_E2_C	ECOD (v294.1)
O	Peripla_BP_3	e3r8bO5	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: Peripla_BP_3	ECOD (v294.1)
M	Peripla_BP_3	e3r8bM5	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: Peripla_BP_3	ECOD (v294.1)
K	Globin	e3r8bK1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Globin	ECOD (v294.1)
I	Tubulin	e3r8bI3	A: a/b three-layered sandwiches	X: POZ domain	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Tubulin	ECOD (v294.1)
G	Globin	e3r8bG1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Globin	ECOD (v294.1)
E	Globin	e3r8bE1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Globin	ECOD (v294.1)
C	Globin	e3r8bC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Globin	ECOD (v294.1)
A	Globin	e3r8bA1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Globin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
P	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
N	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
L	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
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)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
O	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
O	2.40.50.110	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
M	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
M	2.40.50.110	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
K	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
K	2.40.50.110	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
I	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
I	2.40.50.110	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
G	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
G	2.40.50.110	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
E	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
E	2.40.50.110	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
C	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
C	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
B, D, F, H, J B, D, F, H, J, L, N, P	G5-8	V-BETA	Rattus norvegicus (Norway rat)	TRBV5*01, TRBJ	V-DOMAIN V-BETA	TR	(V-BETA)	IMGT (202614-0)
A, C, E, G, I A, C, E, G, I, K, M, O	Superantigen enterotoxin type B (SEB)	Toxin	Staphylococcus aureus	entB*01	R-LIKE-DOMAIN SAG-DOMAIN	TOX	Protein	IMGT (202614-0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L, N, P	G5-8	-	-	-
A, C, E, G, I A, C, E, G, I, K, M, O	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, C, E, G, I A, C, E, G, I, K, M, O	IPR006123	Staphylococcal/Streptococcal toxin, beta-grasp domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR006177	Staphylococcal/streptococcal toxin, bacterial	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR006126	Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site	Conserved Site
A, C, E, G, I A, C, E, G, I, K, M, O	IPR016091	Superantigen toxin, C-terminal	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR006173	Staphylococcal/Streptococcal toxin, OB-fold	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR013307	Superantigen, staphylococcal/streptococcal toxin, bacterial	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR008992	Enterotoxin	Homologous Superfamily