4K4C | pdb_00004k4c

X-ray crystal structure of E. coli YbdB complexed with phenacyl-CoA

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	d4k4cd_	Alpha and beta proteins (a+b)	Thioesterase/thiol ester dehydrase-isomerase	Thioesterase/thiol ester dehydrase-isomerase	PaaI/YdiI-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d4k4cc_	Alpha and beta proteins (a+b)	Thioesterase/thiol ester dehydrase-isomerase	Thioesterase/thiol ester dehydrase-isomerase	PaaI/YdiI-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4k4cb_	Alpha and beta proteins (a+b)	Thioesterase/thiol ester dehydrase-isomerase	Thioesterase/thiol ester dehydrase-isomerase	PaaI/YdiI-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d4k4ca_	Alpha and beta proteins (a+b)	Thioesterase/thiol ester dehydrase-isomerase	Thioesterase/thiol ester dehydrase-isomerase	PaaI/YdiI-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Thioesterase/thiol ester dehydrase-isomerase-like	8035791	3000149	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thioesterase/thiol ester dehydrase-isomerase-like	8035791	3000149	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thioesterase/thiol ester dehydrase-isomerase-like	8035791	3000149	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thioesterase/thiol ester dehydrase-isomerase-like	8035791	3000149	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)
D	HrpJ	e4k4cD1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Ribosomal protein L14-related	T: Ribosomal protein L14-related	F: HrpJ	ECOD (v294.1)
C	HrpJ	e4k4cC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Ribosomal protein L14-related	T: Ribosomal protein L14-related	F: HrpJ	ECOD (v294.1)
B	HrpJ	e4k4cB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Ribosomal protein L14-related	T: Ribosomal protein L14-related	F: HrpJ	ECOD (v294.1)
A	HrpJ	e4k4cA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Ribosomal protein L14-related	T: Ribosomal protein L14-related	F: HrpJ	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.10.129.10	Alpha Beta	Roll	Thiol Ester Dehydrase	Chain A	CATH (4.3.0)
C	3.10.129.10	Alpha Beta	Roll	Thiol Ester Dehydrase	Chain A	CATH (4.3.0)
B	3.10.129.10	Alpha Beta	Roll	Thiol Ester Dehydrase	Chain A	CATH (4.3.0)
A	3.10.129.10	Alpha Beta	Roll	Thiol Ester Dehydrase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF03061	Thioesterase superfamily (4HBT)	Thioesterase superfamily	This family contains a wide variety of enzymes, principally thioesterases. This family includes 4HBT (EC 3.1.2.23) which catalyses the final step in the biosynthesis of 4-hydroxybenzoate from 4-chlorobenzoate in the soil dwelling microbe Pseudomonas ...	This family contains a wide variety of enzymes, principally thioesterases. This family includes 4HBT (EC 3.1.2.23) which catalyses the final step in the biosynthesis of 4-hydroxybenzoate from 4-chlorobenzoate in the soil dwelling microbe Pseudomonas CBS-3. This family includes various cytosolic long-chain acyl-CoA thioester hydrolases. Long-chain acyl-CoA hydrolases hydrolyse palmitoyl-CoA to CoA and palmitate, they also catalyse the hydrolysis of other long chain fatty acyl-CoA thioesters.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Proofreading thioesterase EntH	1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity hydrolase activity, acting on ester bonds thiolester hydrolase activity deacylase activity hydrolase activity catalytic activity acyl-CoA hydrolase activity identical protein binding protein binding binding	enterobactin biosynthetic process polyketide metabolic process catechol-containing compound metabolic process secondary metabolic process antibiotic biosynthetic process siderophore biosynthetic process antibiotic metabolic process secondary metabolite biosynthetic process siderophore metabolic process lactone biosynthetic process catechol-containing compound biosynthetic process catechol-containing siderophore biosynthetic process macrolide biosynthetic process macrolide metabolic process enterobactin biosynthetic process polyketide metabolic process catechol-containing compound metabolic process secondary metabolic process antibiotic biosynthetic process siderophore biosynthetic process antibiotic metabolic process secondary metabolite biosynthetic process siderophore metabolic process lactone biosynthetic process catechol-containing compound biosynthetic process catechol-containing siderophore biosynthetic process macrolide biosynthetic process macrolide metabolic process biosynthetic process peptide biosynthetic process polyketide biosynthetic process lactone metabolic process phenol-containing compound metabolic process phenol-containing compound biosynthetic process metabolic process cellular process nonribosomal peptide biosynthetic process peptide metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR026576	Proofreading thioesterase EntH	Family
A, B, C, D	IPR029069	HotDog domain superfamily	Homologous Superfamily
A, B, C, D	IPR006683	Thioesterase domain	Domain
A, B, C, D	IPR003736	Phenylacetic acid degradation-related 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.