1RXQ | pdb_00001rxq

YfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology

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)
D	d1rxqd_	All alpha proteins	DinB/YfiT-like putative metalloenzymes	DinB/YfiT-like putative metalloenzymes	YfiT-like putative metal-dependent hydrolases	YfiT	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1rxqc_	All alpha proteins	DinB/YfiT-like putative metalloenzymes	DinB/YfiT-like putative metalloenzymes	YfiT-like putative metal-dependent hydrolases	YfiT	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1rxqb_	All alpha proteins	DinB/YfiT-like putative metalloenzymes	DinB/YfiT-like putative metalloenzymes	YfiT-like putative metal-dependent hydrolases	YfiT	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1rxqa_	All alpha proteins	DinB/YfiT-like putative metalloenzymes	DinB/YfiT-like putative metalloenzymes	YfiT-like putative metal-dependent hydrolases	YfiT	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	DinB/YfiT-like putative metalloenzymes	8038984	3001308	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DinB/YfiT-like putative metalloenzymes	8038984	3001308	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DinB/YfiT-like putative metalloenzymes	8038984	3001308	SCOP2B (2022-06-29)
A	SCOP2 Family	YfiT-like putative metal-dependent hydrolases	8026605	4002482	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DinB/YfiT-like putative metalloenzymes	8038984	3001308	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)
D		e1rxqD1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (v294.1)
C		e1rxqC1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (v294.1)
B		e1rxqB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (v294.1)
A	DinB_2	e1rxqA1	A: alpha bundles	X: YfiT-like putative metal-dependent hydrolases	H: YfiT-like putative metal-dependent hydrolases	T: YfiT-like putative metal-dependent hydrolases	F: DinB_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.20.120.450	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	dinb family like domain	CATH (4.3.0)
C	1.20.120.450	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	dinb family like domain	CATH (4.3.0)
B	1.20.120.450	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	dinb family like domain	CATH (4.3.0)
A	1.20.120.450	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	dinb family like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF12867	DinB superfamily (DinB_2)	DinB superfamily	The DinB family are an uncharacterised family of potential enzymes. The structure of these proteins is composed of a four helix bundle [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	yfiT	hydrolase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	-	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR024775	Hercynine oxygenase, DinB-like domain	Domain
A, B, C, D	IPR023774	Putative metal-dependent hydrolase YfiT	Family
A, B, C, D	IPR034660	DinB/YfiT-like putative metalloenzymes	Homologous Superfamily

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.