6UC6 | pdb_00006uc6

Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-H11

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody 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)
D	d6uc6d_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
B [auth C]	d6uc6c_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
A	d6uc6a1	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	d6uc6a2	All beta proteins	beta-Trefoil	STI-like	Clostridium neurotoxins, C-terminal domain	Botulinum neurotoxin	(Clostridium botulinum ) [TaxId: 1491 ],	SCOPe (2.08)
C [auth B]	d6uc6b1	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 [auth B]	d6uc6b2	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	SCOP2B Superfamily	STI-like	8042038	3000715	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041452	3000120	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	STI-like	8042038	3000715	SCOP2B (2022-06-29)
C [auth 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)
D	V-set_12	e6uc6D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
B [auth C]	V-set_12	e6uc6C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
A	Toxin_R_bind_N	e6uc6A1	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	Toxin_R_bind_C	e6uc6A2	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 [auth B]	Toxin_R_bind_N	e6uc6B2	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 [auth B]	Toxin_R_bind_C	e6uc6B1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
A	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (utative)
C [auth B]	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
C [auth B]	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (utative)

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
B [auth C], D	VHH JLI-H11	1C-LIKE	Vicugna pacos (alpaca)	IGHV3-301, IGHJ401	V-DOMAIN VH	IG	VH	IMGT (202605-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth C], D	Heavy Chain	IGHV1	-	botulinum neurotoxin type b	SAbDab (2026-02-06)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C], D	JLI-H11	-	-	-
A, C [auth B]	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 extracellular region host cellular component host cell part host cell synapse host cell membrane host cell presynaptic membrane other organism part host intracellular part host cell cytoplasm host intracellular region host cell cytosol host cell cytoplasm part host intracellular membrane-bounded organelle cellular anatomical structure extracellular region host cellular component host cell part host cell synapse host cell membrane host cell presynaptic membrane other organism part host intracellular part host cell cytoplasm host intracellular region host cell cytosol host cell cytoplasm part host intracellular membrane-bounded organelle host intracellular organelle host cell cytoplasmic vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR000395	Botulinum/Tetanus toxin, catalytic chain	Domain
A, C [auth B]	IPR012928	Clostridium neurotoxin, receptor binding N-terminal	Domain
A, C [auth B]	IPR012500	Clostridium neurotoxin, translocation	Domain
A, C [auth B]	IPR011065	Kunitz inhibitor STI-like superfamily	Homologous Superfamily
A, C [auth B]	IPR013104	Clostridium neurotoxin, receptor-binding C-terminal	Domain
A, C [auth B]	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, C [auth B]	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.