5L6M | pdb_00005l6m

Structure of Caulobacter crescentus VapBC1 (VapB1deltaC:VapC1 form)

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e5l6mA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Osmotin-like	T: Osmotin-like	F:	ECOD (v294.1)
E	FCH	e5l6mE1	A: a/b three-layered sandwiches	X: Ntn/PP2C	H: Ntn	T: Penicillin acylase, catalytic domain	F: FCH	ECOD (v294.1)
H	Peptidase_C78	e5l6mH1	A: a/b three-layered sandwiches	X: MocoBD/DmpA-related	H: ferredoxin-like domain in periplasmic region of MacB	T: ferredoxin-like domain in periplasmic region of MacB	F: Peptidase_C78	ECOD (v294.1)
I	Cadherin	e5l6mI1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Osmotin-like	T: CARF (CRISPR-associated Rossmann fold) domains	F: Cadherin	ECOD (v294.1)
L	GLMA_C	e5l6mL1	A: a/b three-layered sandwiches	X: Mog1p/PsbP-like	H: EGF-related	T: TNF receptor-like	F: GLMA_C	ECOD (v294.1)
D	PemK_toxin	e5l6mD1	A: a/b three-layered sandwiches	X: SH3	H: SH3	T: SH3	F: PemK_toxin	ECOD (v294.1)
B	TP_methylase	e5l6mB1	A: a/b three-layered sandwiches	X: Tetrapyrrole methylase C-terminal domain-like	H: Tetrapyrrole methylase C-terminal domain	T: Tetrapyrrole methylase C-terminal domain	F: TP_methylase	ECOD (v294.1)
C	TP_methylase	e5l6mC1	A: a/b three-layered sandwiches	X: Tetrapyrrole methylase C-terminal domain-like	H: Tetrapyrrole methylase C-terminal domain	T: Tetrapyrrole methylase C-terminal domain	F: TP_methylase	ECOD (v294.1)
G	TP_methylase	e5l6mG1	A: a/b three-layered sandwiches	X: Tetrapyrrole methylase C-terminal domain-like	H: Tetrapyrrole methylase C-terminal domain	T: Tetrapyrrole methylase C-terminal domain	F: TP_methylase	ECOD (v294.1)
J	TP_methylase	e5l6mJ1	A: a/b three-layered sandwiches	X: Tetrapyrrole methylase C-terminal domain-like	H: Tetrapyrrole methylase C-terminal domain	T: Tetrapyrrole methylase C-terminal domain	F: TP_methylase	ECOD (v294.1)
K	TP_methylase	e5l6mK1	A: a/b three-layered sandwiches	X: Tetrapyrrole methylase C-terminal domain-like	H: Tetrapyrrole methylase C-terminal domain	T: Tetrapyrrole methylase C-terminal domain	F: TP_methylase	ECOD (v294.1)
F	TP_methylase	e5l6mF1	A: a/b three-layered sandwiches	X: Tetrapyrrole methylase C-terminal domain-like	H: Tetrapyrrole methylase C-terminal domain	T: Tetrapyrrole methylase C-terminal domain	F: TP_methylase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
G	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
J	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
K	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, C, F, G, J B, C, F, G, J, K	PF01850	PIN domain (PIN)	PIN domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D, E, H, I A, D, E, H, I, L	VapB family protein	-	-	-
B, C, F, G, J B, C, F, G, J, K	Ribonuclease VapC	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding hydrolase activity catalytic activity nuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity toxin activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, E, H, I A, D, E, H, I, L	IPR037914	SpoVT-AbrB domain superfamily	Homologous Superfamily
B, C, F, G, J B, C, F, G, J, K	IPR002716	PIN domain	Domain
B, C, F, G, J B, C, F, G, J, K	IPR029060	PIN-like domain superfamily	Homologous Superfamily
B, C, F, G, J B, C, F, G, J, K	IPR022907	VapC family	Family
B, C, F, G, J B, C, F, G, J, K	IPR050556	Type II toxin-antitoxin system RNase	Family

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.