5Y42 | pdb_00005y42

Native-crystal structure of three chain non-toxic type II ribosome inactivating protein purified from the seeds of Trichosanthes anguina

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
F	d5y42f1	All beta proteins	beta-Trefoil	Ricin B-like lectins	automated matches	automated matches	(Trichosanthes anguina ) [TaxId: 50544 ],	SCOPe (2.08)
C	d5y42c1	All beta proteins	beta-Trefoil	Ricin B-like lectins	automated matches	automated matches	(Trichosanthes anguina ) [TaxId: 50544 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Ribosome inactivating proteins (RIP)	8077769	3001164	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribosome inactivating proteins (RIP)	8077769	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)
F	Ricin_B_lectin	e5y42F2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: Ricin_B_lectin	ECOD (1.6)
C	Ricin_B_lectin	e5y42C2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: Ricin_B_lectin	ECOD (1.6)
E	RIP	e5y42E1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
C	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
E	3.40.420.10	Alpha Beta	3-Layer(aba) Sandwich	Ricin (A subunit)	domain 1	CATH (4.3.0)
E	4.10.470.10	Few Secondary Structures	Irregular	Ricin (A Subunit), domain 2	Ricin (A Subunit), domain 2	CATH (4.3.0)
B	3.40.420.10	Alpha Beta	3-Layer(aba) Sandwich	Ricin (A subunit)	domain 1	CATH (4.3.0)
B	4.10.470.10	Few Secondary Structures	Irregular	Ricin (A Subunit), domain 2	Ricin (A Subunit), domain 2	CATH (4.3.0)
D	6.10.250.2640	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	6.10.250.2640	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	Seed lectin	binding carbohydrate binding 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	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	-
B, E	Seed lectin	binding carbohydrate binding 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	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, D	Lectin	binding carbohydrate binding 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	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, F	IPR036041	Ribosome-inactivating protein superfamily	Homologous Superfamily
C, F	IPR016139	Ribosome-inactivating protein, subdomain 2	Homologous Superfamily
C, F	IPR017989	Ribosome-inactivating protein type 1/2	Family
C, F	IPR035992	Ricin B-like lectins	Homologous Superfamily
C, F	IPR016138	Ribosome-inactivating protein, subdomain 1	Homologous Superfamily
C, F	IPR001574	Ribosome-inactivating protein	Family
C, F	IPR000772	Ricin B, lectin domain	Domain
B, E	IPR036041	Ribosome-inactivating protein superfamily	Homologous Superfamily
B, E	IPR016139	Ribosome-inactivating protein, subdomain 2	Homologous Superfamily
B, E	IPR017989	Ribosome-inactivating protein type 1/2	Family
B, E	IPR035992	Ricin B-like lectins	Homologous Superfamily
B, E	IPR016138	Ribosome-inactivating protein, subdomain 1	Homologous Superfamily
B, E	IPR001574	Ribosome-inactivating protein	Family
B, E	IPR000772	Ricin B, lectin domain	Domain
A, D	IPR036041	Ribosome-inactivating protein superfamily	Homologous Superfamily
A, D	IPR016139	Ribosome-inactivating protein, subdomain 2	Homologous Superfamily
A, D	IPR017989	Ribosome-inactivating protein type 1/2	Family
A, D	IPR035992	Ricin B-like lectins	Homologous Superfamily
A, D	IPR016138	Ribosome-inactivating protein, subdomain 1	Homologous Superfamily
A, D	IPR001574	Ribosome-inactivating protein	Family
A, D	IPR000772	Ricin B, lectin domain	Domain