1S3R | pdb_00001s3r

Crystal structure of the human-specific toxin intermedilysin

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
Membrane Protein Annotation: OPM

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1s3rb2	All beta proteins	Perfringolysin C-terminal-like	Perfringolysin C-terminal-like	Perfringolysin C-terminal-like	Intermedilysin C-terminal domain	(Streptococcus intermedius ) [TaxId: 1338 ],	SCOPe (2.08)
B	d1s3rb1	Membrane and cell surface proteins and peptides	Perfringolysin N-terminal-like	Perfringolysin N-terminal-like	Perfringolysin N-terminal-like	Intermedilysin N-terminal domain	(Streptococcus intermedius ) [TaxId: 1338 ],	SCOPe (2.08)
A	d1s3ra2	All beta proteins	Perfringolysin C-terminal-like	Perfringolysin C-terminal-like	Perfringolysin C-terminal-like	Intermedilysin C-terminal domain	(Streptococcus intermedius ) [TaxId: 1338 ],	SCOPe (2.08)
A	d1s3ra1	Membrane and cell surface proteins and peptides	Perfringolysin N-terminal-like	Perfringolysin N-terminal-like	Perfringolysin N-terminal-like	Intermedilysin N-terminal domain	(Streptococcus intermedius ) [TaxId: 1338 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	MAC/CDC-like	8052024	3002081	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CDC membrane-sensing domain-like	8052023	3000285	SCOP2B (2022-06-29)
A	SCOP2 Family	Perfringolysin-like	8052008	4003121	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	MAC/CDC-like	8052024	3002081	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	CDC membrane-sensing domain-like	8052023	3000285	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)
B	TPR_2, TPR_P4H	e1s3rB1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: ARM repeat	T: ARM repeat	F: TPR_2, TPR_P4H	ECOD (v294.1)
A	TPR_2, TPR_P4H	e1s3rA1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: ARM repeat	T: ARM repeat	F: TPR_2, TPR_P4H	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.840.10	Alpha Beta	Alpha-Beta Complex	HIV-1 Reverse Transcriptase	Chain A, domain 3	CATH (4.3.0)
B	3.30.1040.20	Alpha Beta	2-Layer Sandwich	Carboxypeptidase Inhibitor	Chain A	CATH (4.3.0)
B	3.40.30.40	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Perfringolysin	CATH (4.3.0)
B	2.60.40.1430	Mainly Beta	Sandwich	Immunoglobulin-like	Perfringolysin, domain 4	CATH (4.3.0)
A	3.90.840.10	Alpha Beta	Alpha-Beta Complex	HIV-1 Reverse Transcriptase	Chain A, domain 3	CATH (4.3.0)
A	3.30.1040.20	Alpha Beta	2-Layer Sandwich	Carboxypeptidase Inhibitor	Chain A	CATH (4.3.0)
A	3.40.30.40	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Perfringolysin	CATH (4.3.0)
A	2.60.40.1430	Mainly Beta	Sandwich	Immunoglobulin-like	Perfringolysin, domain 4	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	intermedilysin	sterol binding binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding cation binding ion binding metal ion binding toxin activity	biological process involved in interspecies interaction between organisms cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing	host cell plasma membrane host cellular component cellular anatomical structure host cell part host cell membrane other organism part extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR038700	Thiol-activated cytolysin, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR036359	Thiol-activated cytolysin superfamily	Homologous Superfamily
A, B	IPR035390	Thiol-activated cytolysin C-terminal	Domain
A, B	IPR001869	Thiol-activated cytolysin	Family
A, B	IPR036363	Thiol-activated cytolysin, alpha-beta domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Monotopic/peripheral	All beta monotopic/peripheral	Cholesterol-dependent cytolysin	Thiol-activated cytolysin

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.