4P1Y | pdb_00004p1y

Crystal structure of staphylococcal gamma-hemolysin prepore

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: mpstruc

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4p1ya_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	Leukocidin (pore-forming toxin)	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
C	d4p1yc_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	Leukocidin (pore-forming toxin)	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
E	d4p1ye_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	Leukocidin (pore-forming toxin)	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
G	d4p1yg_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	Leukocidin (pore-forming toxin)	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
B	d4p1yb1	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
B	d4p1yb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
D	d4p1yd1	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
D	d4p1yd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
F	d4p1yf1	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
F	d4p1yf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
H	d4p1yh1	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
H	d4p1yh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Leukocidin (pore-forming toxin)	8074055	4003101	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Leukocidin-like	8074056	3000256	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Leukocidin-like	8074056	3000256	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Leukocidin-like	8074056	3000256	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Leukocidin-like	8074056	3000256	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	Epimerase, NmrA	e4p1yA1	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Epimerase, NmrA	ECOD (develop294)
C	Epimerase, NmrA	e4p1yC1	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Epimerase, NmrA	ECOD (develop294)
E	Epimerase, NmrA	e4p1yE1	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Epimerase, NmrA	ECOD (develop294)
G	Epimerase, NmrA	e4p1yG1	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Epimerase, NmrA	ECOD (develop294)
B	Epimerase, NmrA	e4p1yB1	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Epimerase, NmrA	ECOD (develop294)
D	Epimerase, NmrA	e4p1yD1	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Epimerase, NmrA	ECOD (develop294)
F	Epimerase, NmrA	e4p1yF1	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Epimerase, NmrA	ECOD (develop294)
H	Epimerase, NmrA	e4p1yH1	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Epimerase, NmrA	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
E	2.70.240.10	Mainly Beta	Distorted Sandwich	Leukocidin-like	Leukocidin/porin MspA	CATH (4.3.0)
G	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	2.70.240.10	Mainly Beta	Distorted Sandwich	Leukocidin-like	Leukocidin/porin MspA	CATH (4.3.0)
F	2.70.240.10	Mainly Beta	Distorted Sandwich	Leukocidin-like	Leukocidin/porin MspA	CATH (4.3.0)
H	2.70.240.10	Mainly Beta	Distorted Sandwich	Leukocidin-like	Leukocidin/porin MspA	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	Gamma-hemolysin component B	-	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, F, H	Gamma-hemolysin component A	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	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR016183	Leukocidin/Hemolysin toxin	Domain
A, C, E, G	IPR036435	Leukocidin/porin MspA superfamily	Homologous Superfamily
A, C, E, G	IPR003963	Bi-component toxin, staphylococci	Family
B, D, F, H	IPR016183	Leukocidin/Hemolysin toxin	Domain
B, D, F, H	IPR036435	Leukocidin/porin MspA superfamily	Homologous Superfamily
B, D, F, H	IPR003963	Bi-component toxin, staphylococci	Family

Membrane Protein Annotation: OPM OPM Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E A, B, C, D, E, F, G, H	mpstruc	TRANSMEMBRANE PROTEINS: BETA-BARREL	Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes	γ-hemolysin prepore

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.