3M4D | pdb_00003m4d

Crystal structure of the M113N mutant of alpha-hemolysin

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: PDBTM
Membrane Protein Annotation: MemProtMD
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)
G	d3m4dg_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	Leukocidin (pore-forming toxin)	Alpha-hemolysin	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
F	d3m4df_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	Leukocidin (pore-forming toxin)	Alpha-hemolysin	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
E	d3m4de_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	Leukocidin (pore-forming toxin)	Alpha-hemolysin	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
D	d3m4dd_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	Leukocidin (pore-forming toxin)	Alpha-hemolysin	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
C	d3m4dc_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	Leukocidin (pore-forming toxin)	Alpha-hemolysin	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
B	d3m4db_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	Leukocidin (pore-forming toxin)	Alpha-hemolysin	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d3m4da_	Membrane and cell surface proteins and peptides	Leukocidin-like	Leukocidin-like	Leukocidin (pore-forming toxin)	Alpha-hemolysin	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G	SCOP2B Superfamily	Leukocidin-like	8037938	3000256	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Leukocidin-like	8037938	3000256	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Leukocidin-like	8037938	3000256	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Leukocidin-like	8037938	3000256	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Leukocidin-like	8037938	3000256	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Leukocidin-like	8037938	3000256	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Leukocidin-like	8037938	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)
G	PBP	e3m4dG1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)
F	PBP	e3m4dF1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)
E	PBP	e3m4dE1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)
D	PBP	e3m4dD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)
C	PBP	e3m4dC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)
B	PBP	e3m4dB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)
A	PBP	e3m4dA1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G	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)
E	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)
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)
A	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, B, C, D, E A, B, C, D, E, F, G	Alpha-hemolysin	identical protein binding protein binding binding 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, B, C, D, E A, B, C, D, E, F, G	IPR016183	Leukocidin/Hemolysin toxin	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR005831	Aerolysin/haemolysin toxin, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G	IPR036435	Leukocidin/porin MspA superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR003963	Bi-component toxin, staphylococci	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G	MemProtMD	Annotated as membrane protein by MemProtMD

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	mpstruc	TRANSMEMBRANE PROTEINS: BETA-BARREL	Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes	α-hemolysin, M113F mutant

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.