1WDK | pdb_00001wdk

fatty acid beta-oxidation multienzyme complex from Pseudomonas fragi, form I (native2)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	d1wdkb1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	HCDH C-domain-like	Fatty oxidation complex alpha subunit, C-terminal domain	(Pseudomonas fragi ) [TaxId: 296 ],	SCOPe (2.08)
B	d1wdkb3	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	Fatty oxidation complex alpha subunit, middle domain	(Pseudomonas fragi ) [TaxId: 296 ],	SCOPe (2.08)
B	d1wdkb4	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Crotonase-like	Fatty oxidation complex alpha subunit, N-terminal domain	(Pseudomonas fragi ) [TaxId: 296 ],	SCOPe (2.08)
A	d1wdka1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	HCDH C-domain-like	Fatty oxidation complex alpha subunit, C-terminal domain	(Pseudomonas fragi ) [TaxId: 296 ],	SCOPe (2.08)
A	d1wdka3	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	Fatty oxidation complex alpha subunit, middle domain	(Pseudomonas fragi ) [TaxId: 296 ],	SCOPe (2.08)
A	d1wdka4	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Crotonase-like	Fatty oxidation complex alpha subunit, N-terminal domain	(Pseudomonas fragi ) [TaxId: 296 ],	SCOPe (2.08)
D	d1wdkd2	Alpha and beta proteins (a/b)	Thiolase-like	Thiolase-like	Thiolase-related	Fatty oxidation complex beta subunit (3-ketoacyl-CoA thiolase), C-terminal domain	(Pseudomonas fragi ) [TaxId: 296 ],	SCOPe (2.08)
D	d1wdkd1	Alpha and beta proteins (a/b)	Thiolase-like	Thiolase-like	Thiolase-related	Fatty oxidation complex beta subunit (3-ketoacyl-CoA thiolase), N-terminal domain	(Pseudomonas fragi ) [TaxId: 296 ],	SCOPe (2.08)
C	d1wdkc2	Alpha and beta proteins (a/b)	Thiolase-like	Thiolase-like	Thiolase-related	Fatty oxidation complex beta subunit (3-ketoacyl-CoA thiolase), C-terminal domain	(Pseudomonas fragi ) [TaxId: 296 ],	SCOPe (2.08)
C	d1wdkc1	Alpha and beta proteins (a/b)	Thiolase-like	Thiolase-like	Thiolase-related	Fatty oxidation complex beta subunit (3-ketoacyl-CoA thiolase), N-terminal domain	(Pseudomonas fragi ) [TaxId: 296 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8017508	3000048	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ClpP/crotonase	8001546	3000033	SCOP2B (2022-06-29)
A	SCOP2 Family	Crotonase-like	8001140	4000036	SCOP2 (2022-06-29)
A	SCOP2 Family	L-3-hydroxyacyl CoA dehydrogenase (HCDH)-like	8001143	4000107	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ClpP/crotonase	8001546	3000033	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	6-phosphogluconate dehydrogenase-like	8017508	3000048	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Thiolase-like	8041706	3000122	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thiolase-like	8041708	3000122	SCOP2B (2022-06-29)
C	SCOP2 Family	Thiolase-related	8029327	4000245	SCOP2 (2022-06-29)
C	SCOP2 Family	Thiolase-related	8029329	4000245	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Thiolase-like	8041706	3000122	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Thiolase-like	8041708	3000122	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e1wdkB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)
B		e1wdkB3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: FAD_binding_3	F:	ECOD (20:10:01)
B		e1wdkB4	A: HTH	X: HTH	H: winged helix domain	T: EF-hand_1, EF-hand_7	F:	ECOD (20:10:01)
A		e1wdkA1	A: 6-phosphogluconate dehydrogenase C-terminal domain-like	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T:	F:	ECOD (20:10:01)
A		e1wdkA3	A: Rossmann-like	X: Rossmann-related	H: NAD(P)-binding Rossmann-fold domains	T: F420_oxidored	F:	ECOD (20:10:01)
A		e1wdkA4	A: ClpP/crotonase	X: ClpP/crotonase	H: ClpP/crotonase	T: ECH_1	F:	ECOD (20:10:01)
D		e1wdkD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Chal_sti_synt_N	F:	ECOD (20:10:01)
C		e1wdkC2	A: Flavodoxin-like	X: Class I glutamine amidotransferase-like	H: Thiolase-like	T: Thiolase_N, ketoacyl-synt	F:	ECOD (20:10:01)
C		e1wdkC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Chal_sti_synt_N	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	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	1.10.1040.50	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)
A	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	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	1.10.1040.50	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)
D	3.40.47.10	Alpha Beta	3-Layer(aba) Sandwich	Peroxisomal Thiolase	Chain A, domain 1	CATH (4.3.0)
C	3.40.47.10	Alpha Beta	3-Layer(aba) Sandwich	Peroxisomal Thiolase	Chain A, domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Fatty oxidation complex alpha subunit	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 enoyl-CoA hydratase activity hydro-lyase activity 3-hydroxyacyl-CoA dehydratase activity 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 enoyl-CoA hydratase activity hydro-lyase activity 3-hydroxyacyl-CoA dehydratase activity lyase activity catalytic activity carbon-oxygen lyase activity isomerase activity intramolecular oxidoreductase activity, transposing C=C bonds intramolecular oxidoreductase activity delta(3)-delta(2)-enoyl-CoA isomerase activity racemase and epimerase activity, acting on hydroxy acids and derivatives racemase and epimerase activity 3-hydroxybutyryl-CoA epimerase activity 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 long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity	fatty acid metabolic process lipid catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process primary 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 fatty acid metabolic process lipid catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process primary 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 metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process lipid oxidation small molecule catabolic process lipid metabolic process	protein-containing complex fatty acid beta-oxidation multienzyme complex catalytic complex oxidoreductase complex transferase complex
C, D	3-ketoacyl-CoA thiolase	acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity acetyl-CoA C-acyltransferase activity C-acyltransferase activity catalytic activity	cellular response to stimulus catabolic process benzene-containing compound metabolic process response to stimulus oxoacid metabolic process cellular response to xenobiotic stimulus carboxylic acid metabolic process organic acid catabolic process organic acid metabolic process xenobiotic catabolic process xenobiotic metabolic process response to xenobiotic stimulus cellular response to chemical stimulus monocarboxylic acid catabolic process response to chemical cellular response to stimulus catabolic process benzene-containing compound metabolic process response to stimulus oxoacid metabolic process cellular response to xenobiotic stimulus carboxylic acid metabolic process organic acid catabolic process organic acid metabolic process xenobiotic catabolic process xenobiotic metabolic process response to xenobiotic stimulus cellular response to chemical stimulus monocarboxylic acid catabolic process response to chemical carboxylic acid catabolic process phenylacetate catabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process small molecule catabolic process fatty acid metabolic process lipid catabolic process primary metabolic process lipid modification fatty acid catabolic process fatty acid oxidation fatty acid beta-oxidation lipid oxidation lipid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
A, B	IPR050136	Fatty acid oxidation complex subunit alpha	Family
A, B	IPR018376	Enoyl-CoA hydratase/isomerase, conserved site	Conserved Site
A, B	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR006108	3-hydroxyacyl-CoA dehydrogenase, C-terminal	Domain
A, B	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR006180	3-hydroxyacyl-CoA dehydrogenase, conserved site	Conserved Site
A, B	IPR012799	Fatty oxidation complex, alpha subunit FadB	Family
A, B	IPR001753	Enoyl-CoA hydratase/isomerase-like domain	Domain
A, B	IPR006176	3-hydroxyacyl-CoA dehydrogenase, NAD binding	Domain
C, D	IPR050215	3-ketoacyl-CoA thiolase-like	Family
C, D	IPR002155	Thiolase	Family
C, D	IPR016039	Thiolase-like	Homologous Superfamily
C, D	IPR020617	Thiolase, C-terminal	Domain
C, D	IPR020616	Thiolase, N-terminal	Domain
C, D	IPR020613	Thiolase, conserved site	Conserved Site
C, D	IPR012805	Acetyl-CoA C-acyltransferase FadA	Family
C, D	IPR020610	Thiolase, active site	Active Site
C, D	IPR020615	Thiolase, acyl-enzyme intermediate active site	Active Site

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.