1SR4 | pdb_00001sr4

Crystal Structure of the Haemophilus ducreyi cytolethal distending toxin

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)
C	d1sr4c_	All beta proteins	beta-Trefoil	Ricin B-like lectins	Ricin B-like	Cytolethal distending toxin subunit C	([Haemophilus] ducreyi ) [TaxId: 730 ],	SCOPe (2.08)
B	d1sr4b_	Alpha and beta proteins (a+b)	DNase I-like	DNase I-like	DNase I-like	Cytolethal distending toxin subunit B	([Haemophilus] ducreyi ) [TaxId: 730 ],	SCOPe (2.08)
A	d1sr4a_	All beta proteins	beta-Trefoil	Ricin B-like lectins	Ricin B-like	Cytolethal distending toxin subunit A	([Haemophilus] ducreyi ) [TaxId: 730 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	Ricin B-like	8027348	4002005	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Ricin B-like lectins	8039727	3000678	SCOP2 (2022-06-29)
B	SCOP2 Family	DNase I-like	8027350	4002213	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	DNase I-like	8039729	3000957	SCOP2 (2022-06-29)
A	SCOP2 Family	Ricin B-like	8027346	4002005	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ricin B-like lectins	8039725	3000678	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)
C	CDtoxinA	e1sr4C1	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	e1sr4B1	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)
A	CDtoxinA	e1sr4A1	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)
C	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)
A	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
C	PF03498	Cytolethal distending toxin A/C domain (CDtoxinA)	Cytolethal distending toxin A/C domain		Domain
B	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
A	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
C	cytolethal distending toxin protein C	binding carbohydrate binding toxin activity	-	cell periphery cell outer membrane cellular anatomical structure external encapsulating structure membrane cell envelope outer membrane
B	cytolethal distending toxin protein B	catalytic activity	-	-
A	Cytolethal distending toxin subunit A	binding carbohydrate binding toxin activity	-	cell periphery cell outer membrane cellular anatomical structure external encapsulating structure membrane cell envelope outer membrane

InterPro: Protein Family Classification InterPro Database Homepage

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

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C	OPM	Monotopic/peripheral	All beta monotopic/peripheral	Beta-trefoil superfamily	Cytolethal distending toxin A/C family

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.