5K59

Crystal structure of LukGH from Staphylococcus aureus in complex with a neutralising antibody

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
Thera-SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth D]	d5k59d_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	automated matches	automated matches	(Staphylococcus aureus subsp. aureus USA300 ) [TaxId: 367830 ],	SCOPe (2.08)
C	d5k59c_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	automated matches	automated matches	(Staphylococcus aureus subsp. aureus USA300 ) [TaxId: 367830 ],	SCOPe (2.08)
B	d5k59b_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	automated matches	automated matches	(Staphylococcus aureus subsp. aureus USA300 ) [TaxId: 367830 ],	SCOPe (2.08)
D [auth A]	d5k59a_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	automated matches	automated matches	(Staphylococcus aureus subsp. aureus USA300 ) [TaxId: 367830 ],	SCOPe (2.08)
E [auth H]	d5k59h_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth E]	d5k59e_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth L]	d5k59l2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth L]	d5k59l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth F]	d5k59f2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth F]	d5k59f1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(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 [auth D]	SCOP2B Superfamily	Leukocidin-like	8099272	3000256	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Leukocidin-like	8099272	3000256	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Leukocidin-like	8074050	3000256	SCOP2B (2022-06-29)
D [auth A]	SCOP2 Family	Leukocidin (pore-forming toxin)	8074049	4003101	SCOP2 (2022-06-29)
D [auth A]	SCOP2 Superfamily	Leukocidin-like	8074050	3000256	SCOP2 (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 D]	Leukocidin	e5k59D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Leukocidin-like (From Topology)	T: Leukocidin-like	F: Leukocidin	ECOD (1.6)
C	Leukocidin	e5k59C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Leukocidin-like (From Topology)	T: Leukocidin-like	F: Leukocidin	ECOD (1.6)
B	Leukocidin	e5k59B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Leukocidin-like (From Topology)	T: Leukocidin-like	F: Leukocidin	ECOD (1.6)
D [auth A]	Leukocidin	e5k59A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Leukocidin-like (From Topology)	T: Leukocidin-like	F: Leukocidin	ECOD (1.6)
E [auth H]	V-set_8	e5k59H2	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 [auth H]	C1-set_1	e5k59H1	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)
G [auth E]	V-set_8	e5k59E1	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)
G [auth E]	C1-set_1	e5k59E2	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 [auth L]	C1-set_4	e5k59L1	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 [auth L]	V-set	e5k59L2	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)
H [auth F]	C1-set_4	e5k59F1	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)
H [auth F]	V-set	e5k59F2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth D]	2.70.240.10	Mainly Beta	Distorted Sandwich	Leukocidin-like	Leukocidin/porin MspA	CATH (4.3.0)
C	2.70.240.10	Mainly Beta	Distorted Sandwich	Leukocidin-like	Leukocidin/porin MspA	CATH (4.3.0)
B	2.70.240.10	Mainly Beta	Distorted Sandwich	Leukocidin-like	Leukocidin/porin MspA	CATH (4.3.0)
D [auth A]	2.70.240.10	Mainly Beta	Distorted Sandwich	Leukocidin-like	Leukocidin/porin MspA	CATH (4.3.0)
E [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H [auth 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
E [auth H], G [auth E]	Antibody Fab Fragment	VH-CH1	Homo sapiens (human)	IGHV4-3901, IGHV4-3906, IGHV4-3907, IGHJ604, IGHG101, IGHG102, IGHG104, IGHG105	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202446-0)
F [auth L], H [auth F]	Antibody Fab Fragment	L-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ401, IGKJ402, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202446-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E [auth H], G [auth E]	Heavy Chain	IGHV4	-	uncharacterized leukocidin-like protein 1	SAbDab (2024-11-15)
F [auth L], H [auth F]	Light Chain	IGKV1	Kappa	uncharacterized leukocidin-like protein 1	SAbDab (2024-11-15)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
E [auth H], G [auth E]	Berlimatoxumab	Staphylococcus aureus Toxin A	Therapeutic SAbDab (2024-11-15)
F [auth L], H [auth F]	Berlimatoxumab	Staphylococcus aureus Toxin A	Therapeutic SAbDab (2024-11-15)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D], C	PF07968	Leukocidin/Hemolysin toxin family (Leukocidin)	Leukocidin/Hemolysin toxin family	-	Domain
B, D [auth A]	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 D], C	Uncharacterized leukocidin-like protein 2	-	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	cellular anatomical structure extracellular region
B, D [auth A]	Uncharacterized leukocidin-like protein 1	-	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	cellular anatomical structure extracellular region
E [auth H], G [auth E]	Fab heavy chain	-	-	-
F [auth L], H [auth F]	Fab light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], C	IPR016183	Leukocidin/Hemolysin toxin	Domain
A [auth D], C	IPR036435	Leukocidin/porin MspA superfamily	Homologous Superfamily
A [auth D], C	IPR003963	Bi-component toxin, staphylococci	Family
B, D [auth A]	IPR016183	Leukocidin/Hemolysin toxin	Domain
B, D [auth A]	IPR036435	Leukocidin/porin MspA superfamily	Homologous Superfamily
B, D [auth A]	IPR003963	Bi-component toxin, staphylococci	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth D], B, C, D [auth A]	OPM	Transmembrane	Beta-barrel transmembrane	Pore-forming beta-sheet toxins	Aerolysin (n=14,S=14 or n=16,S=16)

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.