5EPM

Ceratotoxin variant in complex with specific antibody Fab fragment

External Resource: Annotation

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	Spider toxins	8061084	4003112	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	omega toxin-like	8061085	3000255	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	omega toxin-like	8061085	3000255	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	V-set_8	e5epmA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
A	C1-set_1	e5epmA2	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)
E	V-set_8	e5epmE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
E	C1-set_1	e5epmE2	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)
B	C1-set_4	e5epmB1	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)
B	V-set	e5epmB2	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)
F	C1-set_4	e5epmF2	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)
F	V-set	e5epmF1	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)
C	Toxin_12	e5epmC1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Toxin_12	ECOD (1.6)
D	Toxin_12	e5epmD1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Toxin_12	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
B	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)

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, E	Fab 6F1	VH-CH1	Mus musculus (house mouse)	IGHV1-6101, IGHV1-5201, IGHJ201, IGHG102	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
B, F	Fab 6F1	L-KAPPA	Mus musculus (house mouse)	IGKV1-11701, IGKJ401, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, E	Heavy Chain	IGHV1	-	beta-theraphotoxin-cm1a	SAbDab (2024-04-19)
B, F	Light Chain	IGKV1	Kappa	beta-theraphotoxin-cm1a	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF07740	Ion channel inhibitory toxin (Toxin_12)	Ion channel inhibitory toxin	This is a family of potent toxins that function as ion-channel inhibitors for several different ions. Omega-Grammotoxin SIA is a VSCC antagonist that inhibits neuronal N- and P-type VSCC responses [1]. Huwentoxin-IV, from the Chinese bird spider, is ...	This is a family of potent toxins that function as ion-channel inhibitors for several different ions. Omega-Grammotoxin SIA is a VSCC antagonist that inhibits neuronal N- and P-type VSCC responses [1]. Huwentoxin-IV, from the Chinese bird spider, is a highly potent neurotoxin that specifically inhibits the neuronal tetrodotoxin-sensitive voltage-gated sodium channel in rat dorsal root ganglion neurons [2]. Hainantoxin-4, from the venom of spider Selenocosmia hainana, adopts an inhibitor cystine knot structural motif like huwentoin-IV, and is a potent antagonist that acts at site 1 on tetrodotoxin-sensitive (TTX-S) sodium channels [3]. Study of the molecular nature of toxin-receptor interactions has helped elucidate the functioning of many ion-channels [4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E	Antibody Fab fragment heavy chain	-	-	-
B, F	Antibody Fab fragment light chain	-	-	-
C, D	Beta-theraphotoxin-Cm1a	molecular function inhibitor activity sodium channel inhibitor activity channel regulator activity transporter inhibitor activity ion channel regulator activity ion channel inhibitor activity molecular function regulator activity sodium channel regulator activity transporter regulator activity channel inhibitor activity calcium channel regulator activity toxin activity	negative regulation of voltage-gated sodium channel activity in another organism modulation of ion channel activity in another organism regulation of molecular function biological process involved in interspecies interaction between organisms negative regulation of molecular function in another organism modulation of voltage-gated sodium channel activity in another organism negative regulation of molecular function biological regulation modulation of molecular function in another organism modulation of process of another organism	extracellular region extracellular space cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR013140	Huwentoxin, conserved site-1	Conserved Site
C, D	IPR011696	Huwentoxin-1 family	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, E	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.