1MDT | pdb_00001mdt

THE REFINED STRUCTURE OF MONOMERIC DIPHTHERIA TOXIN AT 2.3 ANGSTROMS RESOLUTION

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)
A	d1mdta1	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	Diphtheria toxin, C-terminal domain	Diphtheria toxin, C-terminal domain	Diphtheria toxin, C-terminal domain	(Corynephage beta ) [TaxId: 10703 ],	SCOPe (2.08)
A	d1mdta2	Alpha and beta proteins (a+b)	ADP-ribosylation	ADP-ribosylation	ADP-ribosylating toxins	Diphtheria toxin, N-terminal domain	(Corynephage beta ) [TaxId: 10703 ],	SCOPe (2.08)
A	d1mdta3	Membrane and cell surface proteins and peptides	Toxins' membrane translocation domains	Diphtheria toxin, middle domain	Diphtheria toxin, middle domain	Diphtheria toxin, middle domain	(Corynephage beta ) [TaxId: 10703 ],	SCOPe (2.08)
B	d1mdtb1	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	Diphtheria toxin, C-terminal domain	Diphtheria toxin, C-terminal domain	Diphtheria toxin, C-terminal domain	(Corynephage beta ) [TaxId: 10703 ],	SCOPe (2.08)
B	d1mdtb2	Alpha and beta proteins (a+b)	ADP-ribosylation	ADP-ribosylation	ADP-ribosylating toxins	Diphtheria toxin, N-terminal domain	(Corynephage beta ) [TaxId: 10703 ],	SCOPe (2.08)
B	d1mdtb3	Membrane and cell surface proteins and peptides	Toxins' membrane translocation domains	Diphtheria toxin, middle domain	Diphtheria toxin, middle domain	Diphtheria toxin, middle domain	(Corynephage beta ) [TaxId: 10703 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	ADP-ribosylation	8036997	3001208	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Diphtheria toxin, middle domain	8037645	3001959	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Diphtheria toxin, C-terminal domain	8040181	3000694	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Diphtheria toxin, middle domain	8037645	3001959	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Diphtheria toxin, C-terminal domain	8040181	3000694	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ADP-ribosylation	8036997	3001208	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	Alpha-L-AF_C	e1mdtA1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Alpha-L-AF_C	ECOD (v294.1)
A		e1mdtA2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F:	ECOD (v294.1)
A	Met_synt_B12	e1mdtA3	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Met_synt_B12	ECOD (v294.1)
B	Alpha-L-AF_C	e1mdtB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Alpha-L-AF_C	ECOD (v294.1)
B		e1mdtB2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F:	ECOD (v294.1)
B	Met_synt_B12	e1mdtB3	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Met_synt_B12	ECOD (v294.1)

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)

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	-	cellular anatomical structure extracellular region 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.