3MDE | pdb_00003mde

CRYSTAL STRUCTURES OF MEDIUM CHAIN ACYL-COA DEHYDROGENASE FROM PIG LIVER MITOCHONDRIA WITH AND WITHOUT SUBSTRATE

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)
A	d3mdea1	All alpha proteins	Bromodomain-like	Acyl-CoA dehydrogenase C-terminal domain-like	Medium chain acyl-CoA dehydrogenase-like, C-terminal domain	Medium chain acyl-CoA dehydrogenase, C-domain	pig (Sus scrofa ) [TaxId: 9823 ],	SCOPe (2.08)
A	d3mdea2	Multi-domain proteins (alpha and beta)	Acyl-CoA dehydrogenase NM domain-like	Acyl-CoA dehydrogenase NM domain-like	Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains	Medium chain acyl-CoA dehydrogenase, NM domains	pig (Sus scrofa ) [TaxId: 9823 ],	SCOPe (2.08)
B	d3mdeb1	All alpha proteins	Bromodomain-like	Acyl-CoA dehydrogenase C-terminal domain-like	Medium chain acyl-CoA dehydrogenase-like, C-terminal domain	Medium chain acyl-CoA dehydrogenase, C-domain	pig (Sus scrofa ) [TaxId: 9823 ],	SCOPe (2.08)
B	d3mdeb2	Multi-domain proteins (alpha and beta)	Acyl-CoA dehydrogenase NM domain-like	Acyl-CoA dehydrogenase NM domain-like	Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains	Medium chain acyl-CoA dehydrogenase, NM domains	pig (Sus scrofa ) [TaxId: 9823 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Medium chain acyl-CoA dehydrogenase C-terminal domain-like	8024548	4000821	SCOP2 (2022-06-29)
A	SCOP2 Family	Medium chain acyl-CoA dehydrogenase FAD-binding domain-like	8025044	4002751	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Acyl-CoA dehydrogenase C-terminal domain-like	8036927	3001580	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Acyl-CoA dehydrogenase N-terminal lobe-like	8037423	3001701	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Acyl-CoA dehydrogenase N-terminal lobe-like	8037423	3001701	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Acyl-CoA dehydrogenase C-terminal domain-like	8036927	3001580	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)
A	Acyl-CoA_dh_M	e3mdeA1	A: alpha bundles	X: EGF-like	H: PABC(PABP) domain	T: PABC(PABP) domain	F: Acyl-CoA_dh_M	ECOD (develop294)
A		e3mdeA2	A: alpha bundles	X: EGF-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F:	ECOD (develop294)
A	ACOX	e3mdeA3	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: ACOX	ECOD (develop294)
B	Acyl-CoA_dh_M	e3mdeB1	A: alpha bundles	X: EGF-like	H: PABC(PABP) domain	T: PABC(PABP) domain	F: Acyl-CoA_dh_M	ECOD (develop294)
B		e3mdeB2	A: alpha bundles	X: EGF-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F:	ECOD (develop294)
B	ACOX	e3mdeB3	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: ACOX	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.540.10	Mainly Alpha	Orthogonal Bundle	Butyryl-Coa Dehydrogenase, subunit A	domain 1	CATH (4.3.0)
A	2.40.110.10	Mainly Beta	Beta Barrel	Butyryl-CoA Dehydrogenase, subunit A	domain 2	CATH (4.3.0)
A	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
B	1.10.540.10	Mainly Alpha	Orthogonal Bundle	Butyryl-Coa Dehydrogenase, subunit A	domain 1	CATH (4.3.0)
B	2.40.110.10	Mainly Beta	Beta Barrel	Butyryl-CoA Dehydrogenase, subunit A	domain 2	CATH (4.3.0)
B	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02771	Acyl-CoA dehydrogenase, N-terminal domain (Acyl-CoA_dh_N)	Acyl-CoA dehydrogenase, N-terminal domain	The N-terminal domain of Acyl-CoA dehydrogenase is an all-alpha domain.	Domain
A, B	PF02770	Acyl-CoA dehydrogenase, middle domain (Acyl-CoA_dh_M)	Acyl-CoA dehydrogenase, middle domain	Central domain of Acyl-CoA dehydrogenase has a beta-barrel fold.	Domain
A, B	PF00441	Acyl-CoA dehydrogenase, C-terminal domain (Acyl-CoA_dh_1)	Acyl-CoA dehydrogenase, C-terminal domain	C-terminal domain of Acyl-CoA dehydrogenase is an all-alpha, four helical up-and-down bundle.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	MEDIUM CHAIN ACYL-COA DEHYDROGENASE	oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor oxidoreductase activity acyl-CoA dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding medium-chain fatty acyl-CoA dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor oxidoreductase activity acyl-CoA dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding medium-chain fatty acyl-CoA dehydrogenase activity identical protein binding protein binding	developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development monosaccharide metabolic process regulation of cellular process gluconeogenesis regulation of primary metabolic process regulation of small molecule metabolic process developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development monosaccharide metabolic process regulation of cellular process gluconeogenesis regulation of primary metabolic process regulation of small molecule metabolic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process regulation of biosynthetic process carbohydrate metabolic process regulation of biological process small molecule biosynthetic process carbohydrate biosynthetic process biological regulation hexose metabolic process primary metabolic process monosaccharide biosynthetic process hexose biosynthetic process biosynthetic process regulation of gluconeogenesis metabolic process cellular process regulation of carbohydrate biosynthetic process regulation of metabolic process glucose metabolic process response to stimulus response to stress response to abiotic stimulus response to cold response to temperature stimulus carnitine metabolic process modified amino acid metabolic process carnitine metabolic process, CoA-linked amino-acid betaine metabolic process fatty acid metabolic process lipid catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process lipid modification organic acid metabolic process organic acid catabolic process fatty acid catabolic process monocarboxylic acid catabolic process fatty acid oxidation carboxylic acid catabolic process fatty acid beta-oxidation monocarboxylic acid metabolic process lipid oxidation small molecule catabolic process lipid metabolic process heart development cellular developmental process cardiac muscle tissue development cardiac muscle cell differentiation muscle cell differentiation tissue development cardiocyte differentiation striated muscle tissue development circulatory system development muscle structure development cell differentiation striated muscle cell differentiation muscle tissue development amino-acid betaine biosynthetic process carnitine biosynthetic process modified amino acid biosynthetic process medium-chain fatty acid catabolic process medium-chain fatty acid metabolic process fatty acid beta-oxidation using acyl-CoA dehydrogenase post-embryonic development glucan biosynthetic process polysaccharide biosynthetic process energy derivation by oxidation of organic compounds glycogen metabolic process generation of precursor metabolites and energy glycogen biosynthetic process macromolecule biosynthetic process polysaccharide metabolic process glucan metabolic process energy reserve metabolic process macromolecule metabolic process response to nutrient levels response to starvation	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure mitochondrion membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane axon membrane-bounded organelle mitochondrial membrane intracellular anatomical structure mitochondrion membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane axon cell projection neuron projection plasma membrane bounded cell projection membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036250	Acyl-CoA dehydrogenase-like, C-terminal	Homologous Superfamily
A, B	IPR037069	Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR009100	Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily	Homologous Superfamily
A, B	IPR034180	Medium-chain specific acyl-CoA dehydrogenase	Family
A, B	IPR009075	Acyl-CoA dehydrogenase/oxidase, C-terminal	Domain
A, B	IPR006089	Acyl-CoA dehydrogenase, conserved site	Conserved Site
A, B	IPR013786	Acyl-CoA dehydrogenase/oxidase, N-terminal	Domain
A, B	IPR006091	Acyl-CoA dehydrogenase/oxidase, middle domain	Domain
A, B	IPR046373	Acyl-CoA oxidase/dehydrogenase, middle domain superfamily	Homologous Superfamily
A, B	IPR050741	Acyl-CoA_dehydrogenase	Unknown

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.