3RTJ | pdb_00003rtj

Crystal structure of ricin bound with dinucleotide ApG

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)
C [auth B]	d3rtjb1	All beta proteins	beta-Trefoil	Ricin B-like lectins	automated matches	automated matches	(Ricinus communis ) [TaxId: 3988 ],	SCOPe (2.08)
B [auth A]	d3rtja_	Alpha and beta proteins (a+b)	Ribosome inactivating proteins (RIP)	Ribosome inactivating proteins (RIP)	Plant cytotoxins	Ricin A-chain	(Ricinus communis ) [TaxId: 3988 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth B]	SCOP2B Superfamily	Ricin B-like lectins	8042020	3000678	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Ricin B-like lectins	8042019	3000678	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Ribosome inactivating proteins (RIP)	8041968	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)
C [auth B]	Pkinase, APH	e3rtjB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Pkinase, APH	ECOD (v294.1)
B [auth A]	Pkinase, APH	e3rtjA1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Pkinase, APH	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth B]	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
B [auth A]	3.40.420.10	Alpha Beta	3-Layer(aba) Sandwich	Ricin (A subunit)	domain 1	CATH (4.3.0)
B [auth A]	4.10.470.10	Few Secondary Structures	Irregular	Ricin (A Subunit), domain 2	Ricin (A Subunit), domain 2	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth B]	Ricin B chain	binding carbohydrate binding toxin activity 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 adenyl ribonucleotide binding nucleotide binding binding carbohydrate binding toxin activity 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 adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding cation binding AMP binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	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 biological process involved in interspecies interaction between organisms disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing response to stimulus defense response response to stress	-
B [auth A]	Ricin A chain	binding carbohydrate binding toxin activity 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 adenyl ribonucleotide binding nucleotide binding binding carbohydrate binding toxin activity 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 adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding cation binding AMP binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	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 biological process involved in interspecies interaction between organisms disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing response to stimulus defense response response to stress	-
A [auth D]	RNA (5'-R(APG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth B]	IPR016139	Ribosome-inactivating protein, subdomain 2	Homologous Superfamily
C [auth B]	IPR016138	Ribosome-inactivating protein, subdomain 1	Homologous Superfamily
C [auth B]	IPR001574	Ribosome-inactivating protein	Family
C [auth B]	IPR036041	Ribosome-inactivating protein superfamily	Homologous Superfamily
C [auth B]	IPR017988	Ribosome-inactivating protein conserved site	Conserved Site
C [auth B]	IPR017989	Ribosome-inactivating protein type 1/2	Family
C [auth B]	IPR035992	Ricin B-like lectins	Homologous Superfamily
C [auth B]	IPR000772	Ricin B, lectin domain	Domain
B [auth A]	IPR016139	Ribosome-inactivating protein, subdomain 2	Homologous Superfamily
B [auth A]	IPR016138	Ribosome-inactivating protein, subdomain 1	Homologous Superfamily
B [auth A]	IPR001574	Ribosome-inactivating protein	Family
B [auth A]	IPR036041	Ribosome-inactivating protein superfamily	Homologous Superfamily
B [auth A]	IPR017988	Ribosome-inactivating protein conserved site	Conserved Site
B [auth A]	IPR017989	Ribosome-inactivating protein type 1/2	Family
B [auth A]	IPR035992	Ricin B-like lectins	Homologous Superfamily
B [auth A]	IPR000772	Ricin B, lectin domain	Domain

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.