4PZE | pdb_00004pze

Crystal structure of (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 in complex with acetoacetyl-CoA

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)
I	d4pzei2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
I	d4pzei1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
H	d4pzeh2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
H	d4pzeh1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
G	d4pzeg2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
G	d4pzeg1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
F	d4pzef2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
F	d4pzef1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
E	d4pzee2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
E	d4pzee1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
D	d4pzed2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
D	d4pzed1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
C	d4pzec2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
C	d4pzec1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
B	d4pzeb2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
B	d4pzeb1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
A	d4pzea2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
A	d4pzea1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
I	3HCDH	e4pzeI2	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: 3HCDH	ECOD (1.6)
I	3HCDH_N	e4pzeI1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 3HCDH_N	ECOD (1.6)
H	3HCDH	e4pzeH1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: 3HCDH	ECOD (1.6)
H	3HCDH_N	e4pzeH2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 3HCDH_N	ECOD (1.6)
G	3HCDH	e4pzeG1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: 3HCDH	ECOD (1.6)
G	3HCDH_N	e4pzeG2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 3HCDH_N	ECOD (1.6)
F	3HCDH	e4pzeF2	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: 3HCDH	ECOD (1.6)
F	3HCDH_N	e4pzeF1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 3HCDH_N	ECOD (1.6)
E	3HCDH	e4pzeE2	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: 3HCDH	ECOD (1.6)
E	3HCDH_N	e4pzeE1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 3HCDH_N	ECOD (1.6)
D	3HCDH	e4pzeD1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: 3HCDH	ECOD (1.6)
D	3HCDH_N	e4pzeD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 3HCDH_N	ECOD (1.6)
C	3HCDH	e4pzeC2	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: 3HCDH	ECOD (1.6)
C	3HCDH_N	e4pzeC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 3HCDH_N	ECOD (1.6)
B	3HCDH	e4pzeB2	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: 3HCDH	ECOD (1.6)
B	3HCDH_N	e4pzeB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 3HCDH_N	ECOD (1.6)
A	3HCDH	e4pzeA1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: 3HCDH	ECOD (1.6)
A	3HCDH_N	e4pzeA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 3HCDH_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.2.0)
I	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.2.0)
H	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.2.0)
H	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.2.0)
G	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.2.0)
G	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.2.0)
F	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.2.0)
F	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.2.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.2.0)
E	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.2.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.2.0)
D	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.2.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.2.0)
C	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.2.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.2.0)
B	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.2.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.2.0)
A	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.2.0)

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, I	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, I	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, I	3-Hydroxyacyl-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 catalytic activity (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity	fatty acid metabolic process oxoacid metabolic process carboxylic acid metabolic process primary metabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process organic acid metabolic process lipid metabolic 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, I	IPR006108	3-hydroxyacyl-CoA dehydrogenase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR013328	6-phosphogluconate dehydrogenase, domain 2	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR006180	3-hydroxyacyl-CoA dehydrogenase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR006176	3-hydroxyacyl-CoA dehydrogenase, NAD binding	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I	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.