4CHG

Crystal structure of VapBC15 complex from Mycobacterium tuberculosis

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G	SCOP2B Superfamily	VapB antitoxin-like	8092312	3002586	SCOP2B (2022-06-29)
H	SCOP2 Family	VapB antitoxin-like	8045870	4004733	SCOP2 (2022-06-29)
H	SCOP2 Superfamily	VapB antitoxin-like	8092312	3002586	SCOP2 (2022-06-29)
I	SCOP2B Superfamily	VapB antitoxin-like	8092312	3002586	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	VapB antitoxin-like	8092312	3002586	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	PIN	e4chgA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: PIN	ECOD (1.6)
B	PIN	e4chgB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: PIN	ECOD (1.6)
C	PIN	e4chgC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: PIN	ECOD (1.6)
E	PIN	e4chgE1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: PIN	ECOD (1.6)
F	PIN	e4chgF1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: PIN	ECOD (1.6)
D	PIN	e4chgD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: PIN	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
B	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
C	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
E	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
F	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
D	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF01850	PIN domain (PIN)	PIN domain	-	Domain
G, H, I, J	PF09957	Bacterial antitoxin of type II TA system, VapB (VapB_antitoxin)	Bacterial antitoxin of type II TA system, VapB	VapB is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is VapC, Pfam:PF05016. The family contains several related antitoxins from Cyanobacteria and Actinobacterial families. Antitoxins of this class carry an N-terminal ribb ...	VapB is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is VapC, Pfam:PF05016. The family contains several related antitoxins from Cyanobacteria and Actinobacterial families. Antitoxins of this class carry an N-terminal ribbon-helix-helix domain, RHH, that is highly conserved across all type II bacterial antitoxins, which dimerises with the RHH domain of a second VapB molecule. A hinge section follows the RHH, with an additional pair of flexible alpha helices at the C-terminus. This C-terminus is the Toxin-binding region of the dimer, and so is specific to the cognate toxin, whereas the RHH domain has the specific function of lying across the RNA-binding groove of the toxin dimer and inactivating the active-site - a more general function of all antitoxins.	Domain

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	PROBABLE RIBONUCLEASE VAPC15	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity	regulation of biological process regulation of growth negative regulation of growth negative regulation of biological process biological regulation growth response to decreased oxygen levels response to stimulus response to hypoxia response to stress response to oxygen levels response to abiotic stimulus	-
G, H, I, J	ANTITOXIN VAPB15	cation binding ion binding binding metal ion binding small molecule binding	positive regulation of growth regulation of biological process regulation of growth positive regulation of biological process biological regulation growth response to decreased oxygen levels response to stimulus response to hypoxia response to stress response to oxygen levels response to abiotic stimulus	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR002716	PIN domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR029060	PIN-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR022907	VapC family	Family
G, H, I, J	IPR019239	Bacterial antitoxin of type II TA system, VapB	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.