2Q3N

Agglutinin from Abrus Precatorius (APA-I)

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2q3na1	Alpha and beta proteins (a+b)	Ribosome inactivating proteins (RIP)	Ribosome inactivating proteins (RIP)	Plant cytotoxins	Agglutinin-1 chain A	(Abrus precatorius ) [TaxId: 3816 ],	SCOPe (2.08)
B	d2q3nb1	All beta proteins	beta-Trefoil	Ricin B-like lectins	Ricin B-like	Agglutinin-1 chain B	(Abrus precatorius ) [TaxId: 3816 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Plant cytotoxins	8022823	4002385	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribosome inactivating proteins (RIP)	8035203	3001164	SCOP2 (2022-06-29)
B	SCOP2 Family	Ricin B-like	8022827	4002005	SCOP2 (2022-06-29)
B	SCOP2 Family	Ricin B-like	8022828	4002005	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Ricin B-like lectins	8035207	3000678	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Ricin B-like lectins	8035208	3000678	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)
A	RIP	e2q3nA1	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	Ricin_B_lectin	e2q3nB1	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)

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 (4.3.0)
A	4.10.470.10	Few Secondary Structures	Irregular	Ricin (A Subunit), domain 2	Ricin (A Subunit), domain 2	CATH (4.3.0)
B	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00161	Ribosome inactivating protein (RIP)	Ribosome inactivating protein	-	Domain
B	PF00652	Ricin-type beta-trefoil lectin domain (Ricin_B_lectin)	Ricin-type beta-trefoil lectin domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Agglutinin-1 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	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 positive regulation of apoptotic process in another organism modulation of apoptotic process in another organism biological process involved in interspecies interaction between organisms positive regulation of biological process regulation of programmed cell death regulation of killing of cells of another organism disruption of cell in another organism modulation of process of another organism positive regulation of cellular process killing of cells of another organism positive regulation of programmed cell death regulation of apoptotic process cell death positive regulation of apoptotic process regulation of cell killing apoptotic process disruption of anatomical structure in another organism programmed cell death cell killing heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules cell adhesion cell-cell adhesion cell-cell adhesion via plasma-membrane adhesion molecules response to stimulus defense response response to stress	-
B	Agglutinin-1 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	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 positive regulation of apoptotic process in another organism modulation of apoptotic process in another organism biological process involved in interspecies interaction between organisms positive regulation of biological process regulation of programmed cell death regulation of killing of cells of another organism disruption of cell in another organism modulation of process of another organism positive regulation of cellular process killing of cells of another organism positive regulation of programmed cell death regulation of apoptotic process cell death positive regulation of apoptotic process regulation of cell killing apoptotic process disruption of anatomical structure in another organism programmed cell death cell killing heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules cell adhesion cell-cell adhesion cell-cell adhesion via plasma-membrane adhesion molecules response to stimulus defense response response to stress	-

InterPro: Protein Family Classification InterPro Database Homepage

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

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.