2NZ9 | pdb_00002nz9

Crystal structure of botulinum neurotoxin type A complexed with monoclonal antibody AR2

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
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)
C	d2nz9c1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2nz9c2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2nz9e1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2nz9e2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2nz9d1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2nz9d2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2nz9d3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d2nz9f1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d2nz9f2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d2nz9f3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	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	8042037	3000715	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041451	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Clostridium neurotoxins, coiled-coil domain	8039654	3001677	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8044155	3001975	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8044155	3001975	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Clostridium neurotoxins, coiled-coil domain	8039654	3001677	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041451	3000120	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	STI-like	8042037	3000715	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)
C	C1-set_4	e2nz9C2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
C	V-set	e2nz9C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
E	C1-set_4	e2nz9E2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
E	V-set	e2nz9E1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
D	C1-set_1	e2nz9D2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
D	V-set_10	e2nz9D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
F	C1-set_1	e2nz9F2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
F	V-set_10	e2nz9F1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
A	Toxin_R_bind_N	e2nz9A1	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	e2nz9A2	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)
A	Toxin_trans	e2nz9A3	A: alpha complex topology	X: Botulinum neurotoxin A heavy chain (From Topology)	H: Botulinum neurotoxin A heavy chain (From Topology)	T: Botulinum neurotoxin A heavy chain	F: Toxin_trans	ECOD (1.6)
A	Peptidase_M27	e2nz9A4	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: Peptidase_M27	ECOD (1.6)
B	Toxin_R_bind_N	e2nz9B1	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	e2nz9B2	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_trans	e2nz9B3	A: alpha complex topology	X: Botulinum neurotoxin A heavy chain (From Topology)	H: Botulinum neurotoxin A heavy chain (From Topology)	T: Botulinum neurotoxin A heavy chain	F: Toxin_trans	ECOD (1.6)
B	Peptidase_M27	e2nz9B4	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: Peptidase_M27	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	3.90.1240.10	Alpha Beta	Alpha-Beta Complex	Zincin-like	Metalloproteases ("zincins"), catalytic domain like	CATH (4.3.0)
A	1.20.1120.10	Mainly Alpha	Up-down Bundle	Clostridium botulinum neurotoxin B, "coiled-coil" domain	Clostridium botulinum neurotoxin b, "coiled-coil" domain	CATH (4.3.0)
A	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
A	2.80.10.50	Mainly Beta	Trefoil	Trefoil (Acidic Fibroblast Growth Factor, subunit A)		CATH (4.3.0)
B	3.90.1240.10	Alpha Beta	Alpha-Beta Complex	Zincin-like	Metalloproteases ("zincins"), catalytic domain like	CATH (4.3.0)
B	1.20.1120.10	Mainly Alpha	Up-down Bundle	Clostridium botulinum neurotoxin B, "coiled-coil" domain	Clostridium botulinum neurotoxin b, "coiled-coil" domain	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)

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
C, E	AR2	L-KAPPA	Chimeric (chimeric)	IGKV3-501, IGKJ401, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202543-0)
D, F	AR2	VH-CH1	Chimeric (chimeric)	IGHV5-402, IGHJ401, IGHG101, IGHG102, IGHG1*04	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202543-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, E	Light Chain	IGKV3	Kappa	botulinum neurotoxin type a	SAbDab (2025-11-07)
D, F	Heavy Chain	IGHV5	-	botulinum neurotoxin type a	SAbDab (2025-11-07)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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 tra ...	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 domain 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, B	PF07952	Clostridium neurotoxin, Translocation domain (Toxin_trans)	Clostridium neurotoxin, Translocation domain	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]. Subsequent to cell surface binding and receptor mediated endocytosis of the neurotoxin, an acid induced conformational change in the neurotoxin translocation domain is believed to allow the domain to penetrate the endosome and from a pore, thereby facilitating the passage of the catalytic domain across the membrane into the cytosol [1]. The structure of the translocation reveals a pair of helices that are 105 Angstroms long and is structurally distinct from other pore forming toxins [1].	Domain
A, B	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 tran ...	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 domain 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
A, B	PF01742	Clostridial neurotoxin zinc protease (Peptidase_M27)	Clostridial neurotoxin zinc protease	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, E	AR2 monoclonal antibody	-	-	-
D, F	AR2 monoclonal antibody	-	-	-
A, B	Botulinum neurotoxin type A	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 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 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 other organism part host cell synapse host cell presynaptic membrane host intracellular part host cell cytoplasm host intracellular region host cell cytosol cellular anatomical structure membrane extracellular region host cell plasma membrane host cellular component host cell part host cell membrane other organism part host cell synapse host cell presynaptic membrane 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, B	IPR000395	Botulinum/Tetanus toxin, catalytic chain	Domain
A, B	IPR012928	Clostridium neurotoxin, receptor binding N-terminal	Domain
A, B	IPR012500	Clostridium neurotoxin, translocation	Domain
A, B	IPR011065	Kunitz inhibitor STI-like superfamily	Homologous Superfamily
A, B	IPR013104	Clostridium neurotoxin, receptor-binding C-terminal	Domain
A, B	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, 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.