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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	TPK_B1_binding	e1qmdA1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: TPK_B1_binding	ECOD (develop294)
A	PAP2	e1qmdA2	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: PAP2	ECOD (develop294)
B	TPK_B1_binding	e1qmdB1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: TPK_B1_binding	ECOD (develop294)
B	PAP2	e1qmdB2	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: PAP2	ECOD (develop294)

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	PF00882	Zinc dependent phospholipase C (Zn_dep_PLPC)	Zinc dependent phospholipase C		Domain
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

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 phospholipase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity phosphatidylcholine phospholipase C activity glycerophospholipase activity hydrolase activity C-type glycerophospholipase activity catalytic activity lipase activity cation binding transition metal ion binding zinc ion binding ion binding phosphoric ester hydrolase activity phospholipase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity phosphatidylcholine phospholipase C activity glycerophospholipase activity hydrolase activity C-type glycerophospholipase activity catalytic activity lipase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule 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	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.