4KUH | pdb_00004kuh

Crystal structure of 3-hydroxybutylryl-CoA dehydrogenase with acetoacetyl-CoA from Clostridium butyricum

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
H	d4kuhh2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Clostridium butyricum E4 str. BoNT E BL5262 ) [TaxId: 632245 ],	SCOPe (2.08)
H	d4kuhh1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Clostridium butyricum E4 str. BoNT E BL5262 ) [TaxId: 632245 ],	SCOPe (2.08)
G	d4kuhg2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Clostridium butyricum E4 str. BoNT E BL5262 ) [TaxId: 632245 ],	SCOPe (2.08)
G	d4kuhg1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Clostridium butyricum E4 str. BoNT E BL5262 ) [TaxId: 632245 ],	SCOPe (2.08)
F	d4kuhf2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Clostridium butyricum E4 str. BoNT E BL5262 ) [TaxId: 632245 ],	SCOPe (2.08)
F	d4kuhf1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Clostridium butyricum E4 str. BoNT E BL5262 ) [TaxId: 632245 ],	SCOPe (2.08)
E	d4kuhe2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Clostridium butyricum E4 str. BoNT E BL5262 ) [TaxId: 632245 ],	SCOPe (2.08)
E	d4kuhe1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Clostridium butyricum E4 str. BoNT E BL5262 ) [TaxId: 632245 ],	SCOPe (2.08)
D	d4kuhd2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Clostridium butyricum E4 str. BoNT E BL5262 ) [TaxId: 632245 ],	SCOPe (2.08)
D	d4kuhd1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Clostridium butyricum E4 str. BoNT E BL5262 ) [TaxId: 632245 ],	SCOPe (2.08)
C	d4kuhc2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Clostridium butyricum E4 str. BoNT E BL5262 ) [TaxId: 632245 ],	SCOPe (2.08)
C	d4kuhc1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Clostridium butyricum E4 str. BoNT E BL5262 ) [TaxId: 632245 ],	SCOPe (2.08)
B	d4kuhb2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Clostridium butyricum E4 str. BoNT E BL5262 ) [TaxId: 632245 ],	SCOPe (2.08)
B	d4kuhb1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Clostridium butyricum E4 str. BoNT E BL5262 ) [TaxId: 632245 ],	SCOPe (2.08)
A	d4kuha2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Clostridium butyricum E4 str. BoNT E BL5262 ) [TaxId: 632245 ],	SCOPe (2.08)
A	d4kuha1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Clostridium butyricum E4 str. BoNT E BL5262 ) [TaxId: 632245 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	PemK_toxin	e4kuhH1	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: PemK_toxin	ECOD (v294.1)
G	PemK_toxin	e4kuhG1	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: PemK_toxin	ECOD (v294.1)
F	PemK_toxin	e4kuhF1	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: PemK_toxin	ECOD (v294.1)
E	PemK_toxin	e4kuhE1	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: PemK_toxin	ECOD (v294.1)
D	PemK_toxin	e4kuhD1	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: PemK_toxin	ECOD (v294.1)
C	PemK_toxin	e4kuhC1	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: PemK_toxin	ECOD (v294.1)
B	PemK_toxin	e4kuhB1	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: PemK_toxin	ECOD (v294.1)
A	PemK_toxin	e4kuhA1	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: PemK_toxin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
H	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)
G	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
G	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)
F	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF02737	3-hydroxyacyl-CoA dehydrogenase, NAD binding domain (3HCDH_N)	3-hydroxyacyl-CoA dehydrogenase, NAD binding domain	This family also includes lambda crystallin.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF00725	3-hydroxyacyl-CoA dehydrogenase, C-terminal domain (3HCDH)	3-hydroxyacyl-CoA dehydrogenase, C-terminal domain	This family also includes lambda crystallin. Some proteins include two copies of this domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	3-hydroxybutyryl-CoA dehydrogenase	NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors 3-hydroxybutyryl-CoA dehydrogenase activity catalytic activity	fatty acid metabolic process oxoacid metabolic process short-chain fatty acid metabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process butyrate metabolic process lipid metabolic process lipid catabolic process catabolic process fatty acid metabolic process oxoacid metabolic process short-chain fatty acid metabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process butyrate metabolic process lipid metabolic process lipid catabolic process catabolic process lipid modification organic acid catabolic process fatty acid catabolic process monocarboxylic acid catabolic process fatty acid oxidation carboxylic acid catabolic process fatty acid beta-oxidation lipid oxidation small molecule catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006108	3-hydroxyacyl-CoA dehydrogenase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013328	6-phosphogluconate dehydrogenase, domain 2	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006180	3-hydroxyacyl-CoA dehydrogenase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006176	3-hydroxyacyl-CoA dehydrogenase, NAD binding	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR022694	3-hydroxyacyl-CoA dehydrogenase	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.