3KYG

Crystal structure of VCA0042 (L135R) complexed with c-di-GMP

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3kyga2	All beta proteins	Split barrel-like	PilZ domain-like	PilZ domain	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
A	d3kyga1	All beta proteins	Split barrel-like	PilZ domain-like	PilZ domain-associated domain	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
B	d3kygb2	All beta proteins	Split barrel-like	PilZ domain-like	PilZ domain	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
B	d3kygb1	All beta proteins	Split barrel-like	PilZ domain-like	PilZ domain-associated domain	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PilZ domain-like	8034728	3000480	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PilZ domain-like	8034727	3000480	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PilZ domain-like	8034727	3000480	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PilZ domain-like	8034728	3000480	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	PilZ	e3kygA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PilZ	ECOD (1.6)
A	YcgR_2	e3kygA2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: YcgR_2	ECOD (1.6)
B	PilZ	e3kygB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PilZ	ECOD (1.6)
B	YcgR_2	e3kygB2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: YcgR_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.110.10	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
A	2.40.10.220	Mainly Beta	Beta Barrel	Thrombin, subunit H	predicted glycosyltransferase like domains	CATH (4.3.0)
B	2.30.110.10	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
B	2.40.10.220	Mainly Beta	Beta Barrel	Thrombin, subunit H	predicted glycosyltransferase like domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF07238	PilZ domain (PilZ)	PilZ domain	PilZ is a c-di-GMP binding domain [3] found in widespread cytoplasmic receptors, which is involved in regulation of motility, biofilm formation and virulence of many bacterial pathogens. This domain binds c-di-GMP through RXXXR and [D/N]hSXXG motifs, ...	PilZ is a c-di-GMP binding domain [3] found in widespread cytoplasmic receptors, which is involved in regulation of motility, biofilm formation and virulence of many bacterial pathogens. This domain binds c-di-GMP through RXXXR and [D/N]hSXXG motifs, however, some PilZ domains lack these motifs and do not bind c-di-GMP [6]. Proteins which contain PilZ are known to interact with the flagellar switch-complex proteins FliG and FliM. This interaction results in a reduction of torque generation and induces CCW motor bias [5]. This is the canonical PilZ domain whose structure consists of six beta-strands that form a beta barrel, followed by a long C-terminal alpha-helix [6].	Domain
A, B	PF12945	Flagellar protein YcgR (PilZNR)	Flagellar protein YcgR	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Putative uncharacterized protein VCA0042	guanyl nucleotide binding binding cyclic nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding cyclic-di-GMP binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding guanyl nucleotide binding binding cyclic nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding cyclic-di-GMP binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	-	bacterial-type flagellum basal body cell projection cellular anatomical structure organelle membraneless organelle bacterial-type flagellum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR012349	FMN-binding split barrel	Homologous Superfamily
A, B	IPR009926	Type III secretion system flagellar brake protein YcgR, PilZN domain	Domain
A, B	IPR009875	PilZ domain	Domain

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.