4U6V

Mechanisms of Neutralization of a Human Anti-Alpha Toxin Antibody

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-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)
D [auth K]	d4u6vk_	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 [auth H]	d4u6vh_	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)
B [auth L]	d4u6vl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d4u6vl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth M]	d4u6vm2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth M]	d4u6vm1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth B]	d4u6vb_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	Leukocidin (pore-forming toxin)	Alpha-hemolysin	(Staphylococcus aureus subsp. aureus TCH60 ) [TaxId: 548473 ],	SCOPe (2.08)
C [auth A]	d4u6va_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	Leukocidin (pore-forming toxin)	Alpha-hemolysin	(Staphylococcus aureus subsp. aureus TCH60 ) [TaxId: 548473 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth K]	PF07654	e4u6vK2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
D [auth K]	PF07686	e4u6vK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
A [auth H]	PF07654	e4u6vH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
A [auth H]	PF07686	e4u6vH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B [auth L]	PF07654	e4u6vL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B [auth L]	PF07686	e4u6vL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
E [auth M]	PF07654	e4u6vM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
E [auth M]	PF07686	e4u6vM2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
F [auth B]	PF07968	e4u6vB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Leukocidin-like (From Topology)	T: Leukocidin-like	F: PF07968	ECOD (1.6)
C [auth A]	PF07968	e4u6vA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Leukocidin-like (From Topology)	T: Leukocidin-like	F: PF07968	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth K]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth B]	2.70.240.10	Mainly Beta	Distorted Sandwich	Leukocidin-like	Leukocidin/porin MspA	CATH (4.3.0)
C [auth A]	2.70.240.10	Mainly Beta	Distorted Sandwich	Leukocidin-like	Leukocidin/porin MspA	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 [auth H], D [auth K]	FAB, ANTIGEN BINDING FRAGMENT, HEAVY CHAIN	VH-CH1	Homo sapiens (human)	IGHV3-1301, IGHV3-1304, IGHJ601, IGHJ602, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)
B [auth L], E [auth M]	FAB, ANTIGEN BINDING FRAGMENT, HEAVY CHAIN	L-KAPPA	Homo sapiens (human)	IGKV1-503, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H], D [auth K]	Heavy Chain	IGHV3	-	alpha-hemolysin	SAbDab (2024-04-26)
B [auth L], E [auth M]	Light Chain	IGKV1	Kappa	alpha-hemolysin	SAbDab (2024-04-26)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
A [auth H], D [auth K]	Suvratoxumab	Staphylococcus aureus Toxin A	Therapeutic SAbDab (2024-04-26)
B [auth L], E [auth M]	Suvratoxumab	Staphylococcus aureus Toxin A	Therapeutic SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], F [auth B]	PF07968	Leukocidin/Hemolysin toxin family (Leukocidin)	Leukocidin/Hemolysin toxin family	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H], D [auth K]	Fab, antigen binding fragment, heavy chain	-	-	-
B [auth L], E [auth M]	Fab, antigen binding fragment, light chain	-	-	-
C [auth A], F [auth B]	Alpha-hemolysin	toxin activity	biological process involved in interspecies interaction between organisms cytolysis in another organism cellular process disruption of cell in another organism disruption of anatomical structure in another organism cytolysis killing of cells of another organism cell killing	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], F [auth B]	IPR016183	Leukocidin/Hemolysin toxin	Domain
C [auth A], F [auth B]	IPR005831	Aerolysin/haemolysin toxin, conserved site	Conserved Site
C [auth A], F [auth B]	IPR036435	Leukocidin/porin MspA superfamily	Homologous Superfamily
C [auth A], F [auth B]	IPR003963	Bi-component toxin, staphylococci	Family

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 R01GM133198.