2DDR | pdb_00002ddr

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
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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	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)
B	SCOP2B Superfamily	DNase I-like	8039666	3000957	SCOP2B (2022-06-29)
A	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)
D	Lactamase_B	e2ddrD1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Lactamase_B	ECOD (develop294)
C	Lactamase_B	e2ddrC1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Lactamase_B	ECOD (develop294)
B	Lactamase_B	e2ddrB1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Lactamase_B	ECOD (develop294)
A	Exo_endo_phos	e2ddrA1	A: few secondary structure elements	X: Carbon-nitrogen hydrolase-like	H: DNase I-like	T: DNase I-like	F: Exo_endo_phos	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

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

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 phospholipase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity sphingophospholipase activity hydrolase activity catalytic 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	cellular anatomical structure extracellular region

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 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.