6VX4 | pdb_00006vx4

Density-fitted Model Structure of Antibody Variable Domains of TyTx11 in Complex with Typhoid Toxin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
A [auth K]	d6vx4k_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
H [auth G]	d6vx4g_	Alpha and beta proteins (a+b)	ADP-ribosylation	ADP-ribosylation	automated matches	automated matches	(Salmonella enterica subsp. enterica serovar Typhi str. CT18 ) [TaxId: 220341 ],	SCOPe (2.08)
I [auth F]	d6vx4f_	Alpha and beta proteins (a+b)	DNase I-like	DNase I-like	automated matches	automated matches	(Salmonella enterica subsp. enterica serovar Typhi str. CT18 ) [TaxId: 220341 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H [auth G]	SCOP2 Family	ADP-ribosylating toxins	8102604	4002404	SCOP2 (2022-06-29)
H [auth G]	SCOP2 Superfamily	ADP-ribosylation	8102605	3001208	SCOP2 (2022-06-29)
I [auth F]	SCOP2B Superfamily	DNase I-like	8061769	3000957	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 K]	V-set	e6vx4K1	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 [auth C]	Pertussis_S2S3	e6vx4C1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: Pertussis_S2S3	ECOD (1.6)
D [auth A]	Pertussis_S2S3	e6vx4A1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: Pertussis_S2S3	ECOD (1.6)
E [auth B]	Pertussis_S2S3	e6vx4B1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: Pertussis_S2S3	ECOD (1.6)
F [auth D]	Pertussis_S2S3	e6vx4D1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: Pertussis_S2S3	ECOD (1.6)
G [auth E]	Pertussis_S2S3	e6vx4E1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: Pertussis_S2S3	ECOD (1.6)
C [auth H]	V-set_10	e6vx4H1	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)
H [auth G]	Pertussis_S1	e6vx4G1	A: a+b complex topology	X: ADP-ribosylation (From Topology)	H: ADP-ribosylation (From Topology)	T: ADP-ribosylation	F: Pertussis_S1	ECOD (1.6)
I [auth F]	Exo_endo_phos	e6vx4F1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: DNase I-like (From Topology)	T: DNase I-like	F: Exo_endo_phos	ECOD (1.6)

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 [auth K]	Fab TyTx11, neutralizing	V-KAPPA	Mus musculus (house mouse)	IGKV13-8501, IGKJ201	V-DOMAIN V-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202510-0)
C [auth H]	Fab TyTx11, neutralizing	VH-CH1	Mus musculus (house mouse)	IGHV1-2002, IGHJ401, IGHG101, IGHG102	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202510-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth K]	Light Chain	IGKV13	Kappa	cytolethal distending toxin subunit b \| pertussis toxin-like subunit arta	SAbDab (2025-03-21)
C [auth H]	Heavy Chain	IGHV1	-	cytolethal distending toxin subunit b \| pertussis toxin-like subunit arta	SAbDab (2025-03-21)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C], D [auth A], E [auth B], F [auth D], G [auth E]	PF02918	Pertussis toxin, subunit 2 and 3, C-terminal domain (Pertussis_S2S3)	Pertussis toxin, subunit 2 and 3, C-terminal domain		Domain
H [auth G]	PF02917	Pertussis toxin, subunit 1 (Pertussis_S1)	Pertussis toxin, subunit 1		Domain
I [auth F]	PF03372	Endonuclease/Exonuclease/phosphatase family (Exo_endo_phos)	Endonuclease/Exonuclease/phosphatase family	This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling [1]. This family includes: AP endonuclease proteins EC:4.2.99.18 e.g Swiss:P27695, DNase I proteins EC:3. ...	This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling [1]. This family includes: AP endonuclease proteins EC:4.2.99.18 e.g Swiss:P27695, DNase I proteins EC:3.1.21.1 e.g. Swiss:P24855, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56 Swiss:O43426, Sphingomyelinase EC:3.1.4.12 Swiss:P11889 and Nocturnin Swiss:O35710.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth K]	Variable Domain of Kappa Chain of TyTx11 Antibody	-	-	-
B [auth C], D [auth A], E [auth B], F [auth D], G [auth E]	Pertussis like toxin subunit B	-	-	cellular anatomical structure extracellular region
C [auth H]	Variable Domain of Heavy Chain of Antibody TyTx11	-	-	-
H [auth G]	Pertussis toxin-like subunit ArtA	pentosyltransferase activity NAD+ poly-ADP-ribosyltransferase activity glycosyltransferase activity transferase activity catalytic activity	-	cellular anatomical structure extracellular region
I [auth F]	Cytolethal distending toxin subunit B	endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity toxin activity	-	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C], D [auth A], E [auth B], F [auth D], G [auth E]	IPR008992	Enterotoxin	Homologous Superfamily
B [auth C], D [auth A], E [auth B], F [auth D], G [auth E]	IPR020063	Bordetella pertussis toxin B, subunit 2/3, C-terminal	Domain
H [auth G]	IPR003898	Bordetella pertussis toxin A	Family
I [auth F]	IPR005135	Endonuclease/exonuclease/phosphatase	Domain
I [auth F]	IPR003539	Cytolethal distending toxin B	Family
I [auth F]	IPR036691	Endonuclease/exonuclease/phosphatase superfamily	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.