1QMD | pdb_00001qmd

calcium bound closed form alpha-toxin from Clostridium perfringens

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: OPM

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1qmda1	All alpha proteins	Phospholipase C/P1 nuclease	Phospholipase C/P1 nuclease	Phospholipase C	Alpha-toxin, N-terminal domain	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
A	d1qmda2	All beta proteins	Lipase/lipooxygenase domain (PLAT/LH2 domain)	Lipase/lipooxygenase domain (PLAT/LH2 domain)	Alpha-toxin, C-terminal domain	Alpha-toxin, C-terminal domain	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
B	d1qmdb1	All alpha proteins	Phospholipase C/P1 nuclease	Phospholipase C/P1 nuclease	Phospholipase C	Alpha-toxin, N-terminal domain	(Clostridium perfringens ) [TaxId: 1502 ],	SCOPe (2.08)
B	d1qmdb2	All beta proteins	Lipase/lipooxygenase domain (PLAT/LH2 domain)	Lipase/lipooxygenase domain (PLAT/LH2 domain)	Alpha-toxin, C-terminal domain	Alpha-toxin, C-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)
A	SCOP2 Family	Phospholipase C	8026385	4001408	SCOP2 (2022-06-29)
A	SCOP2 Family	alpha-toxin, C-terminal domain	8028716	4002405	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Phospholipase C/P1 nuclease	8038764	3001513	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Lipase/lipooxygenase domain (PLAT/LH2 domain)	8041095	3001168	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Lipase/lipooxygenase domain (PLAT/LH2 domain)	8041095	3001168	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phospholipase C/P1 nuclease	8038764	3001513	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	PLAT	e1qmdA1	A: beta sandwiches	X: jelly-roll	H: Lipase/lipooxygenase domain (PLAT/LH2 domain) (From Topology)	T: Lipase/lipooxygenase domain (PLAT/LH2 domain)	F: PLAT	ECOD (1.6)
A	Zn_dep_PLPC	e1qmdA2	A: alpha bundles	X: Phospholipase C/P1 nuclease (From Topology)	H: Phospholipase C/P1 nuclease (From Topology)	T: Phospholipase C/P1 nuclease	F: Zn_dep_PLPC	ECOD (1.6)
B	PLAT	e1qmdB1	A: beta sandwiches	X: jelly-roll	H: Lipase/lipooxygenase domain (PLAT/LH2 domain) (From Topology)	T: Lipase/lipooxygenase domain (PLAT/LH2 domain)	F: PLAT	ECOD (1.6)
B	Zn_dep_PLPC	e1qmdB2	A: alpha bundles	X: Phospholipase C/P1 nuclease (From Topology)	H: Phospholipase C/P1 nuclease (From Topology)	T: Phospholipase C/P1 nuclease	F: Zn_dep_PLPC	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.575.10	Mainly Alpha	Orthogonal Bundle	P1 Nuclease	P1 Nuclease	CATH (4.3.0)
A	2.60.60.20	Mainly Beta	Sandwich	Lipoxygenase-1	PLAT/LH2 domain	CATH (4.3.0)
B	1.10.575.10	Mainly Alpha	Orthogonal Bundle	P1 Nuclease	P1 Nuclease	CATH (4.3.0)
B	2.60.60.20	Mainly Beta	Sandwich	Lipoxygenase-1	PLAT/LH2 domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01477	PLAT/LH2 domain (PLAT)	PLAT/LH2 domain	This domain is found in a variety of membrane or lipid associated proteins. It is called the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain. The known structure of pancreatic lipase shows this domain bind ...	This domain is found in a variety of membrane or lipid associated proteins. It is called the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain. The known structure of pancreatic lipase shows this domain binds to procolipase Pfam:PF01114, which mediates membrane association. So it appears possible that this domain mediates membrane attachment via other protein binding partners. The structure of this domain is known for many members of the family and is composed of a beta sandwich.	Domain
A, B	PF00882	Zinc dependent phospholipase C (Zn_dep_PLPC)	Zinc dependent phospholipase C		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PHOSPHOLIPASE C	phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity phosphatidylcholine phospholipase C activity phospholipase C activity hydrolase activity catalytic activity phospholipase activity lipase activity cation binding transition metal ion binding zinc ion binding ion binding binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity phosphatidylcholine phospholipase C activity phospholipase C activity hydrolase activity catalytic activity phospholipase activity lipase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion 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	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001024	PLAT/LH2 domain	Domain
A, B	IPR008947	Phospholipase C/P1 nuclease domain superfamily	Homologous Superfamily
A, B	IPR029002	Phospholipase C/D	Domain
A, B	IPR036392	PLAT/LH2 domain superfamily	Homologous Superfamily
A, B	IPR001531	Zinc-dependent phospholipase C	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Monotopic/peripheral	All alpha monotopic/peripheral	Phospholipase C/P1 nuclease	Zinc dependent phospholipase C

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.