2RDE | pdb_00002rde

Crystal structure of VCA0042 complexed with c-di-GMP

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2rdeb1	All beta proteins	Split barrel-like	PilZ domain-like	PilZ domain	Hypothetical protein VCA0042, C-terminal domain	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)
B	d2rdeb2	All beta proteins	Split barrel-like	PilZ domain-like	PilZ domain-associated domain	Hypothetical protein VCA0042, N-terminal domain	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)
A	d2rdea1	All beta proteins	Split barrel-like	PilZ domain-like	PilZ domain	Hypothetical protein VCA0042, C-terminal domain	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)
A	d2rdea2	All beta proteins	Split barrel-like	PilZ domain-like	PilZ domain-associated domain	Hypothetical protein VCA0042, N-terminal domain	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	PilZ domain-like	8036822	3000480	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PilZ domain-like	8036820	3000480	SCOP2B (2022-06-29)
A	SCOP2 Family	PilZ domain-like	8024441	4001865	SCOP2 (2022-06-29)
A	SCOP2 Family	PilZ domain-associated domain	8024443	4001875	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PilZ domain-like	8036820	3000480	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PilZ domain-like	8036822	3000480	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)
B	PilZ	e2rdeB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PilZ	ECOD (1.6)
B	YcgR_2	e2rdeB2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: YcgR_2	ECOD (1.6)
A	PilZ	e2rdeA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PilZ	ECOD (1.6)
A	YcgR_2	e2rdeA2	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)
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)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	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	-	-

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.