2F2F

Crystal structure of cytolethal distending toxin (CDT) from Actinobacillus actinomycetemcomitans

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	d2f2fa1	All beta proteins	beta-Trefoil	Ricin B-like lectins	Ricin B-like	Cytolethal distending toxin subunit A	(Aggregatibacter actinomycetemcomitans ) [TaxId: 714 ],	SCOPe (2.08)
D	d2f2fd_	All beta proteins	beta-Trefoil	Ricin B-like lectins	Ricin B-like	Cytolethal distending toxin subunit A	(Aggregatibacter actinomycetemcomitans ) [TaxId: 714 ],	SCOPe (2.08)
B	d2f2fb1	Alpha and beta proteins (a+b)	DNase I-like	DNase I-like	DNase I-like	Cytolethal distending toxin subunit B	(Aggregatibacter actinomycetemcomitans ) [TaxId: 714 ],	SCOPe (2.08)
E	d2f2fe_	Alpha and beta proteins (a+b)	DNase I-like	DNase I-like	DNase I-like	Cytolethal distending toxin subunit B	(Aggregatibacter actinomycetemcomitans ) [TaxId: 714 ],	SCOPe (2.08)
C	d2f2fc1	All beta proteins	beta-Trefoil	Ricin B-like lectins	Ricin B-like	Cytolethal distending toxin subunit C	(Aggregatibacter actinomycetemcomitans ) [TaxId: 714 ],	SCOPe (2.08)
F	d2f2ff_	All beta proteins	beta-Trefoil	Ricin B-like lectins	Ricin B-like	Cytolethal distending toxin subunit C	(Aggregatibacter actinomycetemcomitans ) [TaxId: 714 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Ricin B-like	8028102	4002005	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ricin B-like lectins	8040481	3000678	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Ricin B-like lectins	8040481	3000678	SCOP2B (2022-06-29)
B	SCOP2 Family	DNase I-like	8028104	4002213	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	DNase I-like	8040483	3000957	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	DNase I-like	8040483	3000957	SCOP2B (2022-06-29)
C	SCOP2 Family	Ricin B-like	8028106	4002005	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Ricin B-like lectins	8040485	3000678	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	Ricin B-like lectins	8040485	3000678	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	CDtoxinA	e2f2fA1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: CDtoxinA	ECOD (1.6)
D	CDtoxinA	e2f2fD1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: CDtoxinA	ECOD (1.6)
B	Exo_endo_phos	e2f2fB1	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)
E	Exo_endo_phos	e2f2fE1	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	CDtoxinA	e2f2fC1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: CDtoxinA	ECOD (1.6)
F	CDtoxinA	e2f2fF1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: CDtoxinA	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
D	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
B	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)
E	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)
C	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
F	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF03498	Cytolethal distending toxin A/C domain (CDtoxinA)	Cytolethal distending toxin A/C domain	-	Domain
B, E	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
C, F	PF03498	Cytolethal distending toxin A/C domain (CDtoxinA)	Cytolethal distending toxin A/C domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D	Cytolethal distending toxin A	binding carbohydrate binding toxin activity	-	cell periphery cell outer membrane external encapsulating structure membrane cell envelope outer membrane cellular anatomical entity
B, E	Cytolethal distending toxin B	catalytic activity	-	-
C, F	cytolethal distending toxin C	toxin activity	-	cell periphery cell outer membrane external encapsulating structure membrane cell envelope outer membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR003558	Cytolethal distending toxin A/C	Family
A, D	IPR015957	Cytolethal distending toxin A	Family
A, D	IPR035992	Ricin B-like lectins	Homologous Superfamily
B, E	IPR005135	Endonuclease/exonuclease/phosphatase	Domain
B, E	IPR003539	Cytolethal distending toxin B	Family
B, E	IPR036691	Endonuclease/exonuclease/phosphatase superfamily	Homologous Superfamily
C, F	IPR003558	Cytolethal distending toxin A/C	Family
C, F	IPR035992	Ricin B-like lectins	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 R01GM133198.