2YBR | pdb_00002ybr

Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in complex with Cn2 toxin from the scorpion Centruroides noxius Hoffmann

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)
H	d2ybrh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d2ybrh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2ybre1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2ybre2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2ybrb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2ybrb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d2ybri_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Long-chain scorpion toxins	Scorpion toxin	(Centruroides noxius ) [TaxId: 6878 ],	SCOPe (2.08)
F	d2ybrf_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Long-chain scorpion toxins	Scorpion toxin	(Centruroides noxius ) [TaxId: 6878 ],	SCOPe (2.08)
C	d2ybrc_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Long-chain scorpion toxins	Scorpion toxin	(Centruroides noxius ) [TaxId: 6878 ],	SCOPe (2.08)
G	d2ybrg_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2ybrd_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2ybra_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	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)
I	SCOP2B Superfamily	Scorpion toxin-like	8038170	3000309	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Scorpion toxin-like	8038170	3000309	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Scorpion toxin-like	8038170	3000309	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)
H	V-set	e2ybrH1	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	V-set	e2ybrE1	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)
B	V-set	e2ybrB1	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)
I	Toxin_3	e2ybrI1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Toxin_3	ECOD (1.6)
F	Toxin_3	e2ybrF1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Toxin_3	ECOD (1.6)
C	Toxin_3	e2ybrC1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Toxin_3	ECOD (1.6)
G	V-set_12	e2ybrG1	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)
D	V-set_12	e2ybrD1	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	V-set_12	e2ybrA1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	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)
I	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
F	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
C	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
G	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)
A	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
B, E, H	9004G, anti-Cn2 toxin	V-KAPPA	Homo sapiens (human)	IGKV3D-1101, IGKJ101	V-DOMAIN V-KAPPA	IG	SCFV-HEAVY-KAPPA	IMGT (202543-0)
A, D, G	9004G, anti-Cn2 toxin	VH	Homo sapiens (human)	IGHV3-901, IGHJ301, IGHJ3*02	V-DOMAIN VH	IG	SCFV-HEAVY-KAPPA	IMGT (202543-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, E, H	Light Chain	IGKV3	Kappa	beta-mammal toxin cn2	SAbDab (2025-11-07)
A, D, G	Heavy Chain	IGHV3	-	beta-mammal toxin cn2	SAbDab (2025-11-07)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F, I	PF00537	Scorpion toxin-like domain (Toxin_3)	Scorpion toxin-like domain	This family contains both neurotoxins and plant defensins. The mustard trypsin inhibitor, MTI-2, is plant defensin. It is a potent inhibitor of trypsin with no activity towards chymotrypsin. MTI-2 is toxic for Lepidopteran insects, but has low activ ...	This family contains both neurotoxins and plant defensins. The mustard trypsin inhibitor, MTI-2, is plant defensin. It is a potent inhibitor of trypsin with no activity towards chymotrypsin. MTI-2 is toxic for Lepidopteran insects, but has low activity against aphids [1]. Brazzein is plant defensin-like protein. It is pH-stable, heat-stable and intensely sweet protein [2]. The scorpion toxin (a neurotoxin) binds to sodium channels and inhibits the activation mechanisms of the channels, thereby blocking neuronal transmission. Scorpion toxins bind to sodium channels and inhibit the activation mechanisms of the channels, thereby blocking neuronal transmission	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, E, H	SINGLE CHAIN ANTIBODY FRAGMENT 9004G	-	-	-
C, F, I	BETA-MAMMAL TOXIN CN2	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 toxin activity	response to stimulus defense response response to stress	cellular anatomical structure extracellular region
A, D, G	SINGLE CHAIN ANTIBODY FRAGMENT 9004G	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F, I	IPR036574	Knottin, scorpion toxin-like superfamily	Homologous Superfamily
C, F, I	IPR018218	Scorpion long chain toxin	Family
C, F, I	IPR002061	Scorpion long chain toxin/defensin	Family
C, F, I	IPR003614	Knottins-like	Domain
C, F, I	IPR044062	LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) 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.