6Z1Y

Crystal structure of type-I ribosome-inactivating protein trichobakin (TBK)

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	d6z1ya_	Alpha and beta proteins (a+b)	Ribosome inactivating proteins (RIP)	Ribosome inactivating proteins (RIP)	Plant cytotoxins	automated matches	(Trichosanthes sp. Bac Kan 8-98 ) [TaxId: 118182 ],	SCOPe (2.08)
B	d6z1yb_	Alpha and beta proteins (a+b)	Ribosome inactivating proteins (RIP)	Ribosome inactivating proteins (RIP)	Plant cytotoxins	automated matches	(Trichosanthes sp. Bac Kan 8-98 ) [TaxId: 118182 ],	SCOPe (2.08)
C	d6z1yc_	Alpha and beta proteins (a+b)	Ribosome inactivating proteins (RIP)	Ribosome inactivating proteins (RIP)	Plant cytotoxins	automated matches	(Trichosanthes sp. Bac Kan 8-98 ) [TaxId: 118182 ],	SCOPe (2.08)
D	d6z1yd_	Alpha and beta proteins (a+b)	Ribosome inactivating proteins (RIP)	Ribosome inactivating proteins (RIP)	Plant cytotoxins	automated matches	(Trichosanthes sp. Bac Kan 8-98 ) [TaxId: 118182 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribosome inactivating proteins (RIP)	8093774	3001164	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribosome inactivating proteins (RIP)	8093774	3001164	SCOP2B (2022-06-29)
C	SCOP2 Family	Plant cytotoxins	8093773	4002385	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Ribosome inactivating proteins (RIP)	8093774	3001164	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Ribosome inactivating proteins (RIP)	8093774	3001164	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	PF00161	e6z1yA1	A: a+b two layers	X: RIP/Polo-box domain	H: Ribosome inactivating proteins (RIP) (From Topology)	T: Ribosome inactivating proteins (RIP)	F: PF00161	ECOD (1.6)
B	PF00161	e6z1yB1	A: a+b two layers	X: RIP/Polo-box domain	H: Ribosome inactivating proteins (RIP) (From Topology)	T: Ribosome inactivating proteins (RIP)	F: PF00161	ECOD (1.6)
C	PF00161	e6z1yC1	A: a+b two layers	X: RIP/Polo-box domain	H: Ribosome inactivating proteins (RIP) (From Topology)	T: Ribosome inactivating proteins (RIP)	F: PF00161	ECOD (1.6)
D	PF00161	e6z1yD1	A: a+b two layers	X: RIP/Polo-box domain	H: Ribosome inactivating proteins (RIP) (From Topology)	T: Ribosome inactivating proteins (RIP)	F: PF00161	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.420.10	Alpha Beta	3-Layer(aba) Sandwich	Ricin (A subunit)	domain 1	CATH (utative)
A	4.10.470.10	Few Secondary Structures	Irregular	Ricin (A Subunit), domain 2	Ricin (A Subunit), domain 2	CATH (utative)
B	3.40.420.10	Alpha Beta	3-Layer(aba) Sandwich	Ricin (A subunit)	domain 1	CATH (utative)
B	4.10.470.10	Few Secondary Structures	Irregular	Ricin (A Subunit), domain 2	Ricin (A Subunit), domain 2	CATH (utative)
C	3.40.420.10	Alpha Beta	3-Layer(aba) Sandwich	Ricin (A subunit)	domain 1	CATH (utative)
C	4.10.470.10	Few Secondary Structures	Irregular	Ricin (A Subunit), domain 2	Ricin (A Subunit), domain 2	CATH (utative)
D	3.40.420.10	Alpha Beta	3-Layer(aba) Sandwich	Ricin (A subunit)	domain 1	CATH (utative)
D	4.10.470.10	Few Secondary Structures	Irregular	Ricin (A Subunit), domain 2	Ricin (A Subunit), domain 2	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00161	Ribosome inactivating protein (RIP)	Ribosome inactivating protein	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Trichobakin	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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036041	Ribosome-inactivating protein superfamily	Homologous Superfamily
A, B, C, D	IPR017988	Ribosome-inactivating protein conserved site	Conserved Site
A, B, C, D	IPR016139	Ribosome-inactivating protein, subdomain 2	Homologous Superfamily
A, B, C, D	IPR017989	Ribosome-inactivating protein type 1/2	Family
A, B, C, D	IPR016138	Ribosome-inactivating protein, subdomain 1	Homologous Superfamily
A, B, C, D	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 R01GM133198.