1TB3 | pdb_00001tb3

Crystal Structure Analysis of Recombinant Rat Kidney Long-chain Hydroxy Acid Oxidase

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)
H	d1tb3h_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
G	d1tb3g_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
F	d1tb3f_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E	d1tb3e_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D	d1tb3d_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d1tb3c_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1tb3b_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1tb3a1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	FMN-linked oxidoreductases	Hydroxyacid oxidase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	FMN-linked oxidoreductases	8058062	3000014	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	FMN-linked oxidoreductases	8058062	3000014	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	FMN-linked oxidoreductases	8058062	3000014	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	FMN-linked oxidoreductases	8058062	3000014	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	FMN-linked oxidoreductases	8058062	3000014	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	FMN-linked oxidoreductases	8058062	3000014	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FMN-linked oxidoreductases	8058062	3000014	SCOP2B (2022-06-29)
A	SCOP2 Family	FMN-linked oxidoreductases	8058061	4000080	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FMN-linked oxidoreductases	8058062	3000014	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)
H	IMPDH_1st_1	e1tb3H1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: IMPDH_1st_1	ECOD (1.6)
G	IMPDH_1st_1	e1tb3G1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: IMPDH_1st_1	ECOD (1.6)
F	IMPDH_1st_1	e1tb3F1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: IMPDH_1st_1	ECOD (1.6)
E	IMPDH_1st	e1tb3E1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: IMPDH_1st	ECOD (1.6)
D	IMPDH_1st_1	e1tb3D1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: IMPDH_1st_1	ECOD (1.6)
C	IMPDH_1st_1	e1tb3C1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: IMPDH_1st_1	ECOD (1.6)
B	IMPDH_1st_1	e1tb3B1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: IMPDH_1st_1	ECOD (1.6)
A	IMPDH_1st	e1tb3A1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: IMPDH_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
G	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
F	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
E	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	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	PF01070	FMN-dependent dehydrogenase (FMN_dh)	FMN-dependent dehydrogenase		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	Hydroxyacid oxidase 3	FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor oxidoreductase activity oxidoreductase activity, acting on CH-OH group of donors (S)-2-hydroxy-acid oxidase activity FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor oxidoreductase activity oxidoreductase activity, acting on CH-OH group of donors (S)-2-hydroxy-acid oxidase activity catalytic activity identical protein binding protein binding	benzene-containing compound metabolic process oxoacid metabolic process mandelate metabolic process carboxylic acid metabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process organic acid metabolic process fatty acid metabolic process lipid modification primary metabolic process fatty acid oxidation lipid oxidation benzene-containing compound metabolic process oxoacid metabolic process mandelate metabolic process carboxylic acid metabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process organic acid metabolic process fatty acid metabolic process lipid modification primary metabolic process fatty acid oxidation lipid oxidation lipid metabolic process	peroxisomal matrix membrane-bounded organelle intracellular anatomical structure peroxisome membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle microbody lumen microbody cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR012133	Alpha-hydroxy acid dehydrogenase, FMN-dependent	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR008259	FMN-dependent alpha-hydroxy acid dehydrogenase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR037396	FMN hydroxy acid dehydrogenase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000262	FMN-dependent dehydrogenase	Domain

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.