6U3U

Crystal Structure of Shiga Toxin 2K

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A [auth B]	d6u3ub_	Alpha and beta proteins (a+b)	Ribosome inactivating proteins (RIP)	Ribosome inactivating proteins (RIP)	Shiga toxin, A-chain	Shiga toxin, A-chain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G [auth A]	d6u3ua_	Alpha and beta proteins (a+b)	Ribosome inactivating proteins (RIP)	Ribosome inactivating proteins (RIP)	Shiga toxin, A-chain	Shiga toxin, A-chain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B [auth C]	d6u3uc_	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C [auth D]	d6u3ud_	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D [auth E]	d6u3ue_	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E [auth H]	d6u3uh_	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F [auth I]	d6u3ui_	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H [auth F]	d6u3uf_	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I [auth G]	d6u3ug_	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J	d6u3uj_	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
K	d6u3uk_	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
L	d6u3ul_	All beta proteins	OB-fold	Bacterial enterotoxins	Bacterial AB5 toxins, B-subunits	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Ribosome inactivating proteins (RIP)	8093804	3001164	SCOP2B (2022-06-29)
G [auth A]	SCOP2 Family	Shiga toxin A-chain	8093803	4002413	SCOP2 (2022-06-29)
G [auth A]	SCOP2 Superfamily	Ribosome inactivating proteins (RIP)	8093804	3001164	SCOP2 (2022-06-29)
B [auth C]	SCOP2B Superfamily	Bacterial enterotoxins	8093814	3000434	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Bacterial enterotoxins	8093814	3000434	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Bacterial enterotoxins	8093814	3000434	SCOP2B (2022-06-29)
E [auth H]	SCOP2B Superfamily	Bacterial enterotoxins	8093814	3000434	SCOP2B (2022-06-29)
F [auth I]	SCOP2B Superfamily	Bacterial enterotoxins	8093814	3000434	SCOP2B (2022-06-29)
H [auth F]	SCOP2B Superfamily	Bacterial enterotoxins	8093814	3000434	SCOP2B (2022-06-29)
I [auth G]	SCOP2B Superfamily	Bacterial enterotoxins	8093814	3000434	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Bacterial enterotoxins	8093814	3000434	SCOP2B (2022-06-29)
K	SCOP2 Family	Bacterial AB5 toxins B-subunits	8093813	4001827	SCOP2 (2022-06-29)
K	SCOP2 Superfamily	Bacterial enterotoxins	8093814	3000434	SCOP2 (2022-06-29)
L	SCOP2B Superfamily	Bacterial enterotoxins	8093814	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)
A [auth B]	RIP	e6u3uB1	A: a+b two layers	X: RIP/Polo-box domain	H: Ribosome inactivating proteins (RIP) (From Topology)	T: Ribosome inactivating proteins (RIP)	F: RIP	ECOD (1.6)
G [auth A]	RIP	e6u3uA1	A: a+b two layers	X: RIP/Polo-box domain	H: Ribosome inactivating proteins (RIP) (From Topology)	T: Ribosome inactivating proteins (RIP)	F: RIP	ECOD (1.6)
B [auth C]	SLT_beta	e6u3uC1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: SLT_beta	ECOD (1.6)
C [auth D]	SLT_beta	e6u3uD1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: SLT_beta	ECOD (1.6)
D [auth E]	SLT_beta	e6u3uE1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: SLT_beta	ECOD (1.6)
E [auth H]	SLT_beta	e6u3uH1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: SLT_beta	ECOD (1.6)
F [auth I]	SLT_beta	e6u3uI1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: SLT_beta	ECOD (1.6)
H [auth F]	SLT_beta	e6u3uF1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: SLT_beta	ECOD (1.6)
I [auth G]	SLT_beta	e6u3uG1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: SLT_beta	ECOD (1.6)
J	SLT_beta	e6u3uJ1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: SLT_beta	ECOD (1.6)
K	SLT_beta	e6u3uK1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: SLT_beta	ECOD (1.6)
L	SLT_beta	e6u3uL1	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)
A [auth B]	3.40.420.10	Alpha Beta	3-Layer(aba) Sandwich	Ricin (A subunit)	domain 1	CATH (utative)
A [auth B]	4.10.470.10	Few Secondary Structures	Irregular	Ricin (A Subunit), domain 2	Ricin (A Subunit), domain 2	CATH (utative)
G [auth A]	3.40.420.10	Alpha Beta	3-Layer(aba) Sandwich	Ricin (A subunit)	domain 1	CATH (utative)
G [auth A]	4.10.470.10	Few Secondary Structures	Irregular	Ricin (A Subunit), domain 2	Ricin (A Subunit), domain 2	CATH (utative)
B [auth C]	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (utative)
C [auth D]	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (utative)
D [auth E]	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (utative)
E [auth H]	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (utative)
F [auth I]	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (utative)
H [auth F]	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (utative)
I [auth G]	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (utative)
J	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (utative)
K	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (utative)
L	2.40.50.70	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], G [auth A]	PF00161	Ribosome inactivating protein (RIP)	Ribosome inactivating protein	-	Domain
B [auth C], C [auth D], D [auth E], E [auth H], F [auth I], B [auth C], C [auth D], D [auth E], E [auth H], F [auth I], H [auth F], I [auth G], J, K, L	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 s ...	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
A [auth B], G [auth A]	Shiga toxin 2K subunit A	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 cellular biosynthetic process organonitrogen compound biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation organic substance metabolic process organic substance biosynthetic process 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 organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular 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	-
B [auth C], C [auth D], D [auth E], E [auth H], F [auth I], B [auth C], C [auth D], D [auth E], E [auth H], F [auth I], H [auth F], I [auth G], J, K, L	Shiga toxin 2K subunit B	-	biological process involved in interspecies interaction between organisms symbiont-mediated cytolysis of host cell disruption of cell in another organism hemolysis by symbiont of host erythrocytes 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	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], G [auth A]	IPR036041	Ribosome-inactivating protein superfamily	Homologous Superfamily
A [auth B], G [auth A]	IPR016331	Shiga-like toxin, subunit A	Family
A [auth B], G [auth A]	IPR017988	Ribosome-inactivating protein conserved site	Conserved Site
A [auth B], G [auth A]	IPR016139	Ribosome-inactivating protein, subdomain 2	Homologous Superfamily
A [auth B], G [auth A]	IPR016138	Ribosome-inactivating protein, subdomain 1	Homologous Superfamily
A [auth B], G [auth A]	IPR001574	Ribosome-inactivating protein	Family
B [auth C], C [auth D], D [auth E], E [auth H], F [auth I], B [auth C], C [auth D], D [auth E], E [auth H], F [auth I], H [auth F], I [auth G], J, K, L	IPR008992	Enterotoxin	Homologous Superfamily
B [auth C], C [auth D], D [auth E], E [auth H], F [auth I], B [auth C], C [auth D], D [auth E], E [auth H], F [auth I], H [auth F], I [auth G], J, K, L	IPR003189	Shiga-like toxin, beta subunit	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.