5VID

Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.0671.2

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 [auth D]	d5vidd1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Clostridium neurotoxins, the second last domain	Botulinum neurotoxin	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
A [auth D]	d5vidd2	All beta proteins	beta-Trefoil	STI-like	Clostridium neurotoxins, C-terminal domain	Botulinum neurotoxin	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
C	d5vidc1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Clostridium neurotoxins, the second last domain	Botulinum neurotoxin	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
C	d5vidc2	All beta proteins	beta-Trefoil	STI-like	Clostridium neurotoxins, C-terminal domain	Botulinum neurotoxin	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
D [auth A]	d5vida1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Clostridium neurotoxins, the second last domain	Botulinum neurotoxin	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
D [auth A]	d5vida2	All beta proteins	beta-Trefoil	STI-like	Clostridium neurotoxins, C-terminal domain	Botulinum neurotoxin	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
E	d5vide1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Clostridium neurotoxins, the second last domain	Botulinum neurotoxin	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
E	d5vide2	All beta proteins	beta-Trefoil	STI-like	Clostridium neurotoxins, C-terminal domain	Botulinum neurotoxin	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
B	d5vidb1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Clostridium neurotoxins, the second last domain	Botulinum neurotoxin	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
B	d5vidb2	All beta proteins	beta-Trefoil	STI-like	Clostridium neurotoxins, C-terminal domain	Botulinum neurotoxin	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth D]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041452	3000120	SCOP2B (2022-06-29)
A [auth D]	SCOP2B Superfamily	STI-like	8042038	3000715	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041452	3000120	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	STI-like	8042038	3000715	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	STI-like	8042038	3000715	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041452	3000120	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	STI-like	8042038	3000715	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041452	3000120	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	STI-like	8042038	3000715	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041452	3000120	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 [auth D]	Toxin_R_bind_N	e5vidD2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Toxin_R_bind_N	ECOD (1.6)
A [auth D]	Toxin_R_bind_C	e5vidD1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: Toxin_R_bind_C	ECOD (1.6)
C	Toxin_R_bind_N	e5vidC2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Toxin_R_bind_N	ECOD (1.6)
C	Toxin_R_bind_C	e5vidC1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: Toxin_R_bind_C	ECOD (1.6)
D [auth A]	Toxin_R_bind_N	e5vidA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Toxin_R_bind_N	ECOD (1.6)
D [auth A]	Toxin_R_bind_C	e5vidA2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: Toxin_R_bind_C	ECOD (1.6)
E	Toxin_R_bind_N	e5vidE2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Toxin_R_bind_N	ECOD (1.6)
E	Toxin_R_bind_C	e5vidE1	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: Toxin_R_bind_C	ECOD (1.6)
B	Toxin_R_bind_N	e5vidB1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Toxin_R_bind_N	ECOD (1.6)
B	Toxin_R_bind_C	e5vidB2	A: beta duplicates or obligate multimers	X: beta-Trefoil (From Topology)	H: beta-Trefoil (From Topology)	T: beta-Trefoil	F: Toxin_R_bind_C	ECOD (1.6)
F	UNK_F_TYPE	e5vidF1	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: UNK_F_TYPE	ECOD (1.6)
G	UNK_F_TYPE	e5vidG1	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: UNK_F_TYPE	ECOD (1.6)
H	UNK_F_TYPE	e5vidH1	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: UNK_F_TYPE	ECOD (1.6)
I	UNK_F_TYPE	e5vidI1	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth D]	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
A [auth D]	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
C	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
D [auth A]	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D [auth A]	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
E	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
E	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
B	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	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 [auth D], B, C, D [auth A], E	PF07951	Clostridium neurotoxin, C-terminal receptor binding (Toxin_R_bind_C)	Clostridium neurotoxin, C-terminal receptor binding	The Clostridium neurotoxin family is composed of tetanus neurotoxins and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (Pfam:PF01742), the central tr ...	The Clostridium neurotoxin family is composed of tetanus neurotoxins and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (Pfam:PF01742), the central translocation domains and two receptor binding domains [1]. This domains is the C-terminal receptor binding domain, which adopts a modified beta-trefoil fold with a six stranded beta-barrel and a beta-hairpin triplet capping the domain [1]. The first step in the intoxication process is a binding event between this domains and the pre-synaptic nerve ending [1].	Domain
A [auth D], B, C, D [auth A], E	PF07953	Clostridium neurotoxin, N-terminal receptor binding (Toxin_R_bind_N)	Clostridium neurotoxin, N-terminal receptor binding	The Clostridium neurotoxin family is composed of tetanus neurotoxin and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (Pfam:PF01742), the central tra ...	The Clostridium neurotoxin family is composed of tetanus neurotoxin and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (Pfam:PF01742), the central translocation domains and two receptor binding domains [1]. This domains is the N-terminal receptor binding domain,which is comprised of two seven-stranded beta-sheets sandwiched together to form a jelly role motif [1]. The role of this domain in receptor binding appears to be indirect.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D], B, C, D [auth A], E	Botulinum neurotoxin type B	binding lipid binding macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity metallopeptidase activity catalytic activity endopeptidase activity binding lipid binding macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity metallopeptidase activity catalytic activity endopeptidase activity toxin activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane extracellular region host cell plasma membrane host cellular component host cell part host cell membrane host cell synapse host cell presynaptic membrane host intracellular part host cell cytoplasm host intracellular region host cell cytosol host cell cytoplasm part cellular anatomical structure membrane extracellular region host cell plasma membrane host cellular component host cell part host cell membrane host cell synapse host cell presynaptic membrane host intracellular part host cell cytoplasm host intracellular region host cell cytosol host cell cytoplasm part host cell cytoplasmic vesicle host intracellular membrane-bounded organelle host intracellular organelle
F, G, H, I	Bot.0671.2	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], B, C, D [auth A], E	IPR000395	Botulinum/Tetanus toxin, catalytic chain	Domain
A [auth D], B, C, D [auth A], E	IPR012928	Clostridium neurotoxin, receptor binding N-terminal	Domain
A [auth D], B, C, D [auth A], E	IPR012500	Clostridium neurotoxin, translocation	Domain
A [auth D], B, C, D [auth A], E	IPR011065	Kunitz inhibitor STI-like superfamily	Homologous Superfamily
A [auth D], B, C, D [auth A], E	IPR013104	Clostridium neurotoxin, receptor-binding C-terminal	Domain
A [auth D], B, C, D [auth A], E	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A [auth D], B, C, D [auth A], E	IPR036248	Clostridium neurotoxin, translocation domain	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.