6X6H | pdb_00006x6h

Structure of Shiga toxin 2 with a C-terminal peptide of ribosomal P stalk proteins

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G [auth F]	SCOP2B Superfamily	Bacterial enterotoxins	8099974	3000434	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	Bacterial enterotoxins	8099974	3000434	SCOP2B (2022-06-29)
E [auth D]	SCOP2B Superfamily	Bacterial enterotoxins	8099974	3000434	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	Bacterial enterotoxins	8099974	3000434	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Bacterial enterotoxins	8099974	3000434	SCOP2B (2022-06-29)
A [auth A1]	SCOP2 Family	Shiga toxin, A-chain	8097213	4002413	SCOP2 (2022-06-29)
A [auth A1]	SCOP2 Superfamily	Ribosome inactivating proteins (RIP)	8097214	3001164	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
G [auth F]	Ldh_1_C	e6x6hF1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.1)
F [auth E]	Ldh_1_C	e6x6hE1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.1)
E [auth D]	Ldh_1_C	e6x6hD1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.1)
D [auth C]	Ldh_1_C	e6x6hC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.1)
C [auth B]	Ldh_1_C	e6x6hB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ldh_1_C	ECOD (v294.1)
B [auth A2]	SBP_bac_1	e6x6hA201	A: a/b three-layered sandwiches	X: Rossmann-like	H: all-alpha NTP pyrophosphatases	T: Hypothetical protein AF_0060	F: SBP_bac_1	ECOD (v294.1)
A [auth A1]	SBP_bac_1	e6x6hA101	A: a/b three-layered sandwiches	X: Rossmann-like	H: all-alpha NTP pyrophosphatases	T: Hypothetical protein AF_0060	F: SBP_bac_1	ECOD (v294.1)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H [auth P]	P11 peptide	-	-	-
C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	Shiga toxin 2 B subunit	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	cellular anatomical structure extracellular region
B [auth A2]	rRNA N-glycosylase	hydrolase activity, acting on glycosyl bonds rRNA N-glycosylase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity, acting on a rRNA catalytic activity RNA glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds toxin activity	regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process	-
A [auth A1]	rRNA N-glycosylase	hydrolase activity, acting on glycosyl bonds rRNA N-glycosylase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity, acting on a rRNA catalytic activity RNA glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds toxin activity	regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	IPR008992	Enterotoxin	Homologous Superfamily
C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	IPR003189	Shiga-like toxin, beta subunit	Family
B [auth A2]	IPR036041	Ribosome-inactivating protein superfamily	Homologous Superfamily
B [auth A2]	IPR016331	Shiga-like toxin, subunit A	Family
B [auth A2]	IPR017988	Ribosome-inactivating protein conserved site	Conserved Site
B [auth A2]	IPR016139	Ribosome-inactivating protein, subdomain 2	Homologous Superfamily
B [auth A2]	IPR016138	Ribosome-inactivating protein, subdomain 1	Homologous Superfamily
B [auth A2]	IPR001574	Ribosome-inactivating protein	Family
A [auth A1]	IPR036041	Ribosome-inactivating protein superfamily	Homologous Superfamily
A [auth A1]	IPR016331	Shiga-like toxin, subunit A	Family
A [auth A1]	IPR017988	Ribosome-inactivating protein conserved site	Conserved Site
A [auth A1]	IPR016139	Ribosome-inactivating protein, subdomain 2	Homologous Superfamily
A [auth A1]	IPR016138	Ribosome-inactivating protein, subdomain 1	Homologous Superfamily
A [auth A1]	IPR001574	Ribosome-inactivating protein	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.