7VHD | pdb_00007vhd

Crystal structure of the STX2a complexed with R4A peptide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

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)	8099972	3001164	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Bacterial enterotoxins	8097164	3000434	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Bacterial enterotoxins	8097164	3000434	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Bacterial enterotoxins	8097164	3000434	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Bacterial enterotoxins	8097164	3000434	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Bacterial enterotoxins	8097164	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		e7vhdA1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: FKBP_C	F:	ECOD (20:10:01)
B		e7vhdB1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: FKBP_C	F:	ECOD (20:10:01)
C		e7vhdC1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: FKBP_C	F:	ECOD (20:10:01)
D		e7vhdD1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: FKBP_C	F:	ECOD (20:10:01)
E		e7vhdE1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: FKBP_C	F:	ECOD (20:10:01)
F		e7vhdF1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: FKBP_C	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00161	Ribosome inactivating protein (RIP)	Ribosome inactivating protein		Domain
B, C, D, E, F	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 su ...	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	rRNA N-glycosylase	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 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, C, D, E, F	Shiga toxin 2 B subunit	toxin activity	biological process involved in interspecies interaction between organisms symbiont-mediated cytolysis of host cell symbiont-mediated hemolysis of host erythrocyte disruption of cell in another organism 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	cellular anatomical structure extracellular region
G	ARG-ARG-ARG-ARG-ALA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
G	NH2	RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109

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.