6ACQ | pdb_00006acq

Crystal structure of (S)-3-hydroxybutyryl-CoA dehydrogenase from Clostridium acetobutylicum, apo form

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)
F	d6acqf2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Clostridium acetobutylicum ATCC 824 ) [TaxId: 272562 ],	SCOPe (2.08)
F	d6acqf1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Clostridium acetobutylicum ATCC 824 ) [TaxId: 272562 ],	SCOPe (2.08)
F	d6acqf3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Clostridium acetobutylicum ATCC 824 ) [TaxId: 272562 ],	SCOPe (2.08)
E	d6acqe2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Clostridium acetobutylicum ATCC 824 ) [TaxId: 272562 ],	SCOPe (2.08)
E	d6acqe1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Clostridium acetobutylicum ATCC 824 ) [TaxId: 272562 ],	SCOPe (2.08)
D	d6acqd2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Clostridium acetobutylicum ATCC 824 ) [TaxId: 272562 ],	SCOPe (2.08)
D	d6acqd1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Clostridium acetobutylicum ATCC 824 ) [TaxId: 272562 ],	SCOPe (2.08)
C	d6acqc2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Clostridium acetobutylicum ATCC 824 ) [TaxId: 272562 ],	SCOPe (2.08)
C	d6acqc1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Clostridium acetobutylicum ATCC 824 ) [TaxId: 272562 ],	SCOPe (2.08)
B	d6acqb2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Clostridium acetobutylicum ATCC 824 ) [TaxId: 272562 ],	SCOPe (2.08)
B	d6acqb1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Clostridium acetobutylicum ATCC 824 ) [TaxId: 272562 ],	SCOPe (2.08)
B	d6acqb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Clostridium acetobutylicum ATCC 824 ) [TaxId: 272562 ],	SCOPe (2.08)
A	d6acqa2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Clostridium acetobutylicum ATCC 824 ) [TaxId: 272562 ],	SCOPe (2.08)
A	d6acqa1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Clostridium acetobutylicum ATCC 824 ) [TaxId: 272562 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	TGF_beta	e6acqF1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: TGF_beta	ECOD (v294.1)
E	Bromodomain	e6acqE1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: Bromodomain	ECOD (v294.1)
D	Bromodomain	e6acqD1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: Bromodomain	ECOD (v294.1)
C	Bromodomain	e6acqC1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: Bromodomain	ECOD (v294.1)
B	Bromodomain	e6acqB1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: Bromodomain	ECOD (v294.1)
A	Bromodomain	e6acqA1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: Bromodomain	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	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	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	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	IPR006108	3-hydroxyacyl-CoA dehydrogenase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR013328	6-phosphogluconate dehydrogenase, domain 2	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR006180	3-hydroxyacyl-CoA dehydrogenase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR006176	3-hydroxyacyl-CoA dehydrogenase, NAD binding	Domain
A, B, C, D, E A, B, C, D, E, F	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	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.