1M3I | pdb_00001m3i

Perfringolysin O, new crystal form

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
Membrane Protein Annotation: mpstruc

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d1m3id2	All beta proteins	Perfringolysin C-terminal-like	Perfringolysin C-terminal-like	Perfringolysin C-terminal-like	Perfringolysin C-terminal domain	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
D	d1m3id1	Membrane and cell surface proteins and peptides	Perfringolysin N-terminal-like	Perfringolysin N-terminal-like	Perfringolysin N-terminal-like	Perfringolysin N-terminal domain	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
C	d1m3ic2	All beta proteins	Perfringolysin C-terminal-like	Perfringolysin C-terminal-like	Perfringolysin C-terminal-like	Perfringolysin C-terminal domain	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
C	d1m3ic1	Membrane and cell surface proteins and peptides	Perfringolysin N-terminal-like	Perfringolysin N-terminal-like	Perfringolysin N-terminal-like	Perfringolysin N-terminal domain	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
B	d1m3ib2	All beta proteins	Perfringolysin C-terminal-like	Perfringolysin C-terminal-like	Perfringolysin C-terminal-like	Perfringolysin C-terminal domain	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
B	d1m3ib1	Membrane and cell surface proteins and peptides	Perfringolysin N-terminal-like	Perfringolysin N-terminal-like	Perfringolysin N-terminal-like	Perfringolysin N-terminal domain	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
A	d1m3ia2	All beta proteins	Perfringolysin C-terminal-like	Perfringolysin C-terminal-like	Perfringolysin C-terminal-like	Perfringolysin C-terminal domain	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
A	d1m3ia1	Membrane and cell surface proteins and peptides	Perfringolysin N-terminal-like	Perfringolysin N-terminal-like	Perfringolysin N-terminal-like	Perfringolysin N-terminal domain	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	CDC membrane-sensing domain-like	8037955	3000285	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	MAC/CDC-like	8052018	3002081	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MAC/CDC-like	8052018	3002081	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CDC membrane-sensing domain-like	8037955	3000285	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MAC/CDC-like	8052018	3002081	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CDC membrane-sensing domain-like	8037955	3000285	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MAC/CDC-like	8052018	3002081	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CDC membrane-sensing domain-like	8037955	3000285	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)
D	Thiol_cytolys_C	e1m3iD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Perfringolysin O beta sandwich domain (From Topology)	T: Perfringolysin O beta sandwich domain	F: Thiol_cytolys_C	ECOD (1.6)
D	Thiol_cytolysin	e1m3iD2	A: beta complex topology	X: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains (From Topology)	H: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains (From Topology)	T: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains	F: Thiol_cytolysin	ECOD (1.6)
C	Thiol_cytolys_C	e1m3iC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Perfringolysin O beta sandwich domain (From Topology)	T: Perfringolysin O beta sandwich domain	F: Thiol_cytolys_C	ECOD (1.6)
C	Thiol_cytolysin	e1m3iC2	A: beta complex topology	X: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains (From Topology)	H: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains (From Topology)	T: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains	F: Thiol_cytolysin	ECOD (1.6)
B	Thiol_cytolys_C	e1m3iB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Perfringolysin O beta sandwich domain (From Topology)	T: Perfringolysin O beta sandwich domain	F: Thiol_cytolys_C	ECOD (1.6)
B	Thiol_cytolysin	e1m3iB2	A: beta complex topology	X: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains (From Topology)	H: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains (From Topology)	T: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains	F: Thiol_cytolysin	ECOD (1.6)
A	Thiol_cytolys_C	e1m3iA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Perfringolysin O beta sandwich domain (From Topology)	T: Perfringolysin O beta sandwich domain	F: Thiol_cytolys_C	ECOD (1.6)
A	Thiol_cytolysin	e1m3iA2	A: beta complex topology	X: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains (From Topology)	H: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains (From Topology)	T: Membrane attack complex/perforin (MACPF) and cholesterol-dependent cytolysin (CDC) domains	F: Thiol_cytolysin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF17440	Thiol-activated cytolysin beta sandwich domain (Thiol_cytolys_C)	Thiol-activated cytolysin beta sandwich domain	This domain has an immunoglobulin like fold. It is found at the C-terminus of the thiol-activated cytolsin protein.	Domain
A, B, C, D	PF01289	Thiol-activated cytolysin (Thiol_cytolysin)	Thiol-activated cytolysin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	perfringolysin O	sterol binding binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding toxin activity	hemolysis in another organism biological process involved in interspecies interaction between organisms cytolysis in another organism cellular process disruption of cell in another organism disruption of anatomical structure in another organism cytolysis killing of cells of another organism cell killing symbiont-mediated cytolysis of host cell biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated killing of host cell	cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D	mpstruc	TRANSMEMBRANE PROTEINS: BETA-BARREL	Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes	Perfringolysin O (PFO) protomer

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.