4AE1

Crystal structure of diphtheria toxin mutant CRM197 in complex with nicotinamide

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
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	d4ae1a3	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	Diphtheria toxin, C-terminal domain	automated matches	automated matches	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)
A	d4ae1a1	Alpha and beta proteins (a+b)	ADP-ribosylation	ADP-ribosylation	automated matches	automated matches	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)
A	d4ae1a2	Membrane and cell surface proteins and peptides	Toxins' membrane translocation domains	Diphtheria toxin, middle domain	automated matches	automated matches	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)
B	d4ae1b3	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	Diphtheria toxin, C-terminal domain	automated matches	automated matches	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)
B	d4ae1b1	Alpha and beta proteins (a+b)	ADP-ribosylation	ADP-ribosylation	automated matches	automated matches	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)
B	d4ae1b2	Membrane and cell surface proteins and peptides	Toxins' membrane translocation domains	Diphtheria toxin, middle domain	automated matches	automated matches	(Corynebacterium diphtheriae ) [TaxId: 1717 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Diphtheria toxin, C-terminal domain	8040181	3000694	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ADP-ribosylation	8036997	3001208	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Diphtheria toxin, middle domain	8037645	3001959	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Diphtheria toxin, middle domain	8037645	3001959	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ADP-ribosylation	8036997	3001208	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Diphtheria toxin, C-terminal domain	8040181	3000694	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	Diphtheria_R	e4ae1A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: Diphtheria_R	ECOD (1.6)
A	Diphtheria_T	e4ae1A3	A: alpha arrays	X: Toxins' membrane translocation domains	H: Diphtheria toxin, middle domain (From Topology)	T: Diphtheria toxin, middle domain	F: Diphtheria_T	ECOD (1.6)
A	Diphtheria_C	e4ae1A2	A: a+b complex topology	X: ADP-ribosylation (From Topology)	H: ADP-ribosylation (From Topology)	T: ADP-ribosylation	F: Diphtheria_C	ECOD (1.6)
B	Diphtheria_R	e4ae1B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: Diphtheria_R	ECOD (1.6)
B	Diphtheria_T	e4ae1B3	A: alpha arrays	X: Toxins' membrane translocation domains	H: Diphtheria toxin, middle domain (From Topology)	T: Diphtheria toxin, middle domain	F: Diphtheria_T	ECOD (1.6)
B	Diphtheria_C	e4ae1B2	A: a+b complex topology	X: ADP-ribosylation (From Topology)	H: ADP-ribosylation (From Topology)	T: ADP-ribosylation	F: Diphtheria_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.175.10	Alpha Beta	Alpha-Beta Complex	Diphtheria Toxin	domain 1	CATH (4.3.0)
A	1.10.490.40	Mainly Alpha	Orthogonal Bundle	Globin-like	Diphtheria toxin, translocation domain	CATH (4.3.0)
A	2.60.40.700	Mainly Beta	Sandwich	Immunoglobulin-like	Diphtheria toxin, receptor-binding domain	CATH (4.3.0)
B	3.90.175.10	Alpha Beta	Alpha-Beta Complex	Diphtheria Toxin	domain 1	CATH (4.3.0)
B	1.10.490.40	Mainly Alpha	Orthogonal Bundle	Globin-like	Diphtheria toxin, translocation domain	CATH (4.3.0)
B	2.60.40.700	Mainly Beta	Sandwich	Immunoglobulin-like	Diphtheria toxin, receptor-binding domain	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A, B	dipheria toxin mutant CRM197	Toxin	Corynebacterium diphtheriae	CRM197*01	R-LIKE-DOMAIN TOX-DOMAIN	TOX	(TOX-DOMAIN)	IMGT (202443-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02764	Diphtheria toxin, T domain (Diphtheria_T)	Diphtheria toxin, T domain	Central domain of diphtheria toxin is the translocation (T) domain. pH induced conformational change in this domain triggers insertion into the endosomal membrane and facilitates the transfer of the catalytic domain into the cytoplasm.	Domain
A, B	PF02763	Diphtheria toxin, C domain (Diphtheria_C)	Diphtheria toxin, C domain	N-terminal catalytic (C) domain - blocks protein synthesis by transfer of ADP-ribose from NAD to a diphthamide residue of EF-2.	Domain
A, B	PF01324	Diphtheria toxin, R domain (Diphtheria_R)	Diphtheria toxin, R domain	C-terminal receptor binding (R) domain - binds to cell surface receptor, permitting the toxin to enter the cell by receptor mediated endocytosis.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DIPHTHERIA TOXIN	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity pentosyltransferase activity glycosyltransferase activity NAD+-diphthamide ADP-ribosyltransferase activity transferase activity catalytic activity toxin activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups identical protein binding macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity pentosyltransferase activity glycosyltransferase activity NAD+-diphthamide ADP-ribosyltransferase activity transferase activity catalytic activity toxin activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups identical protein binding protein binding binding	-	extracellular region cellular anatomical entity cell periphery plasma membrane membrane extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036799	Diphtheria toxin, receptor-binding domain superfamily	Homologous Superfamily
A, B	IPR000512	Diphtheria toxin (NAD+-dipthamide ADP-ribosyltransferase)	Family
A, B	IPR022404	Diphtheria toxin, receptor-binding domain	Domain
A, B	IPR036801	Diphtheria toxin, translocation domain superfamily	Homologous Superfamily
A, B	IPR022406	Diphtheria toxin, catalytic domain	Domain

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.