2DDR

Crystal structure of sphingomyelinase from Bacillus cereus with calcium ion

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2ddra1	Alpha and beta proteins (a+b)	DNase I-like	DNase I-like	Sphingomyelin phosphodiesterase-like	Sphingomyelin phosphodiesterase C	(Bacillus cereus ) [TaxId: 1396 ],	SCOPe (2.08)
B	d2ddrb_	Alpha and beta proteins (a+b)	DNase I-like	DNase I-like	Sphingomyelin phosphodiesterase-like	automated matches	(Bacillus cereus ) [TaxId: 1396 ],	SCOPe (2.08)
C	d2ddrc_	Alpha and beta proteins (a+b)	DNase I-like	DNase I-like	Sphingomyelin phosphodiesterase-like	automated matches	(Bacillus cereus ) [TaxId: 1396 ],	SCOPe (2.08)
D	d2ddrd_	Alpha and beta proteins (a+b)	DNase I-like	DNase I-like	Sphingomyelin phosphodiesterase-like	automated matches	(Bacillus cereus ) [TaxId: 1396 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	DNase I-like	8039666	3000957	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNase I-like	8039666	3000957	SCOP2B (2022-06-29)
C	SCOP2 Family	Sphingomyelin phosphodiesterase-like	8027287	4000417	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	DNase I-like	8039666	3000957	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	DNase I-like	8039666	3000957	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	Exo_endo_phos	e2ddrA1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: DNase I-like (From Topology)	T: DNase I-like	F: Exo_endo_phos	ECOD (1.6)
B	Exo_endo_phos	e2ddrB1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: DNase I-like (From Topology)	T: DNase I-like	F: Exo_endo_phos	ECOD (1.6)
C	Exo_endo_phos	e2ddrC1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: DNase I-like (From Topology)	T: DNase I-like	F: Exo_endo_phos	ECOD (1.6)
D	Exo_endo_phos	e2ddrD1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: DNase I-like (From Topology)	T: DNase I-like	F: Exo_endo_phos	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)
B	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)
C	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)
D	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF03372	Endonuclease/Exonuclease/phosphatase family (Exo_endo_phos)	Endonuclease/Exonuclease/phosphatase family	This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling [1]. This family includes: AP endonuclease proteins EC:4.2.99.18 e.g Swiss:P27695, DNase I proteins EC:3. ...	This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling [1]. This family includes: AP endonuclease proteins EC:4.2.99.18 e.g Swiss:P27695, DNase I proteins EC:3.1.21.1 e.g. Swiss:P24855, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56 Swiss:O43426, Sphingomyelinase EC:3.1.4.12 Swiss:P11889 and Nocturnin Swiss:O35710.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Sphingomyelin phosphodiesterase	sphingomyelin phosphodiesterase activity phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity hydrolase activity catalytic activity phospholipase activity lipase 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	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR005135	Endonuclease/exonuclease/phosphatase	Domain
A, B, C, D	IPR017766	Sphingomyelinase C/phospholipase C	Family
A, B, C, D	IPR038772	Sphingomyelinase C/Sphingomyelin phosphodiesterase 2-like	Family
A, B, C, D	IPR036691	Endonuclease/exonuclease/phosphatase superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.