4H56 | pdb_00004h56

Crystal structure of the Clostridium perfringens NetB toxin in the membrane inserted form

External Resource: Annotation

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: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Leukocidin-like	8074046	3000256	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Leukocidin-like	8074046	3000256	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Leukocidin-like	8074046	3000256	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Leukocidin-like	8074046	3000256	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Leukocidin-like	8074046	3000256	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Leukocidin-like	8074046	3000256	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Leukocidin-like	8074046	3000256	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Leukocidin-like	8074046	3000256	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Leukocidin-like	8074046	3000256	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Leukocidin-like	8074046	3000256	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Leukocidin-like	8074046	3000256	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Leukocidin-like	8074046	3000256	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Leukocidin-like	8074046	3000256	SCOP2B (2022-06-29)
A	SCOP2 Family	Leukocidin (pore-forming toxin)	8074045	4003101	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Leukocidin-like	8074046	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)
F	14-3-3	e4h56F1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: 14-3-3	ECOD (develop294)
G	14-3-3	e4h56G1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: 14-3-3	ECOD (develop294)
L	14-3-3	e4h56L1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: 14-3-3	ECOD (develop294)
M	14-3-3	e4h56M1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: 14-3-3	ECOD (develop294)
N	14-3-3	e4h56N1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: 14-3-3	ECOD (develop294)
K	14-3-3	e4h56K1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: 14-3-3	ECOD (develop294)
J	14-3-3	e4h56J1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: 14-3-3	ECOD (develop294)
I	14-3-3	e4h56I1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: 14-3-3	ECOD (develop294)
H	14-3-3	e4h56H1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: 14-3-3	ECOD (develop294)
E	14-3-3	e4h56E1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: 14-3-3	ECOD (develop294)
D	14-3-3	e4h56D1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: 14-3-3	ECOD (develop294)
C	14-3-3	e4h56C1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: 14-3-3	ECOD (develop294)
B	14-3-3	e4h56B1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: 14-3-3	ECOD (develop294)
A	Gln-synt_C	e4h56A1	A: alpha bundles	X: Globin-like	H: Ring-building motif I in type III secretion system	T: Ring-building motif I in type III secretion system	F: Gln-synt_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	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)
L	2.70.240.10	Mainly Beta	Distorted Sandwich	Leukocidin-like	Leukocidin/porin MspA	CATH (4.3.0)
M	2.70.240.10	Mainly Beta	Distorted Sandwich	Leukocidin-like	Leukocidin/porin MspA	CATH (4.3.0)
N	2.70.240.10	Mainly Beta	Distorted Sandwich	Leukocidin-like	Leukocidin/porin MspA	CATH (4.3.0)
K	2.70.240.10	Mainly Beta	Distorted Sandwich	Leukocidin-like	Leukocidin/porin MspA	CATH (4.3.0)
J	2.70.240.10	Mainly Beta	Distorted Sandwich	Leukocidin-like	Leukocidin/porin MspA	CATH (4.3.0)
I	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)
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, H, I, J, K, L, M, N	Necrotic enteritis toxin B	cation binding ion binding binding metal ion binding small molecule binding	hemolysis in another organism 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 adhesion of symbiont to host cell surface via host membrane cholesterol adhesion of symbiont to host cell adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction	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, H, I, J, K, L, M, N	IPR016183	Leukocidin/Hemolysin toxin	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR036435	Leukocidin/porin MspA superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	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, I, J, K, L, M, N	OPM	Transmembrane	Beta-barrel transmembrane	Pore-forming beta-sheet toxins	Aerolysin (n=14,S=14 or n=16,S=16)

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	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, H, I, J, K, L, M, N	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, H, I, J, K, L, M, N	mpstruc	TRANSMEMBRANE PROTEINS: BETA-BARREL	Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes	NetB Necrotic B-like enteritis toxin

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.