6FE4 | pdb_00006fe4

Crystal structure of the complex between Shiga toxin Stx2 B subunit and neutralising Nb113

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)
J	d6fe4j1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
J	d6fe4j2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
I	d6fe4i1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
I	d6fe4i2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
H	d6fe4h1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
H	d6fe4h2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
G	d6fe4g1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
G	d6fe4g2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
F	d6fe4f1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
F	d6fe4f2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
E	d6fe4e1	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	Bacteriophage 933W (Escherichia phage 933W ) [TaxId: 10730 ],	SCOPe (2.08)
E	d6fe4e2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Bacteriophage 933W (Escherichia phage 933W ) [TaxId: 10730 ],	SCOPe (2.08)
D	d6fe4d_	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	Bacteriophage 933W (Escherichia phage 933W ) [TaxId: 10730 ],	SCOPe (2.08)
C	d6fe4c1	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	Bacteriophage 933W (Escherichia phage 933W ) [TaxId: 10730 ],	SCOPe (2.08)
C	d6fe4c2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Bacteriophage 933W (Escherichia phage 933W ) [TaxId: 10730 ],	SCOPe (2.08)
B	d6fe4b1	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	Bacteriophage 933W (Escherichia phage 933W ) [TaxId: 10730 ],	SCOPe (2.08)
B	d6fe4b2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Bacteriophage 933W (Escherichia phage 933W ) [TaxId: 10730 ],	SCOPe (2.08)
A	d6fe4a1	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	Bacteriophage 933W (Escherichia phage 933W ) [TaxId: 10730 ],	SCOPe (2.08)
A	d6fe4a2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Bacteriophage 933W (Escherichia phage 933W ) [TaxId: 10730 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Bacterial enterotoxins	8040290	3000434	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Bacterial enterotoxins	8040290	3000434	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Bacterial enterotoxins	8040290	3000434	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Bacterial enterotoxins	8040290	3000434	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Bacterial enterotoxins	8040290	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	V-set_8	e6fe4J1	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)
I	V-set_8	e6fe4I1	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)
H	V-set_8	e6fe4H1	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)
G	V-set_8	e6fe4G1	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)
F	V-set_8	e6fe4F1	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)
E	SLT_beta	e6fe4E1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: SLT_beta	ECOD (1.6)
D	SLT_beta	e6fe4D1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: SLT_beta	ECOD (1.6)
C	SLT_beta	e6fe4C1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: SLT_beta	ECOD (1.6)
B	SLT_beta	e6fe4B1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: SLT_beta	ECOD (1.6)
A	SLT_beta	e6fe4A1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: SLT_beta	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
D	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
C	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
A	2.40.50.70	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
F, G, H, I, J	Fab Nb113, neutralizing	VH	Vicugna pacos (alpaca)	IGHV3S101, IGHJ601	V-DOMAIN VH	IG	VH	IMGT (202546-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
F, G, H, I, J	Heavy Chain	IGHV3	-	shiga-like toxin 2 subunit b	SAbDab (2025-11-28)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF02258	Shiga-like toxin beta subunit (SLT_beta)	Shiga-like toxin beta subunit	This family represents the B subunit of shiga-like toxin (SLT or verotoxin) produced by some strains of E.coli associated with hemorrhagic colitis and hemolytic uremic syndrome. SLT's are composed of one enzymatic A subunit and five cell binding B su ...	This family represents the B subunit of shiga-like toxin (SLT or verotoxin) produced by some strains of E.coli associated with hemorrhagic colitis and hemolytic uremic syndrome. SLT's are composed of one enzymatic A subunit and five cell binding B subunits.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F, G, H, I, J	Nb113	-	-	-
A, B, C, D, E	Shiga-like toxin 2 subunit B	toxin activity	biological process involved in interspecies interaction between organisms symbiont-mediated cytolysis of host cell symbiont-mediated hemolysis of host erythrocyte disruption of cell in another organism cytolysis biological process involved in interaction with host biological process involved in symbiotic interaction cytolysis in another organism cellular process disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing symbiont-mediated modulation of host virulence biological process involved in interspecies interaction between organisms symbiont-mediated cytolysis of host cell symbiont-mediated hemolysis of host erythrocyte disruption of cell in another organism cytolysis biological process involved in interaction with host biological process involved in symbiotic interaction cytolysis in another organism cellular process disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing symbiont-mediated modulation of host virulence symbiont-mediated perturbation of host process modulation of process of another organism	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR008992	Enterotoxin	Homologous Superfamily
A, B, C, D, E	IPR003189	Shiga-like toxin, beta subunit	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.