1KBI | pdb_00001kbi

Crystallographic Study of the Recombinant Flavin-binding Domain of Baker's Yeast Flavocytochrome b2: Comparison with the Intact Wild-type Enzyme

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)
B	d1kbib_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	FMN-linked oxidoreductases	Flavocytochrome b2, C-terminal domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1kbia1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	FMN-linked oxidoreductases	Flavocytochrome b2, C-terminal domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1kbia2	Alpha and beta proteins (a+b)	Cytochrome b5-like heme/steroid binding domain	Cytochrome b5-like heme/steroid binding domain	Cytochrome b5	Flavocytochrome b2, N-terminal domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	FMN-linked oxidoreductases	8017532	3000014	SCOP2B (2022-06-29)
A	SCOP2 Family	FMN-linked oxidoreductases	8003221	4000080	SCOP2 (2022-06-29)
A	SCOP2 Family	Cytochrome b5	8003222	4000144	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FMN-linked oxidoreductases	8017532	3000014	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cytochrome b5-like heme/steroid binding domain	8003822	3000073	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	PF27526	e1kbiB1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: PF27526	ECOD (develop294)
A	Cyt-b5	e1kbiA1	A: a+b two layers	X: Cystatin-like	H: Cytochrome b5-like heme/steroid binding domain	T: Cytochrome b5-like heme/steroid binding domain	F: Cyt-b5	ECOD (develop294)
A	FMN_dh, Glu_synthase	e1kbiA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: FMN_dh, Glu_synthase	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	3.10.120.10	Alpha Beta	Roll	Flavocytochrome B2	Chain A, domain 1	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	PF01070	FMN-dependent dehydrogenase (FMN_dh)	FMN-dependent dehydrogenase		Domain
A, B	PF00173	Cytochrome b5-like Heme/Steroid binding domain (Cyt-b5)	Cytochrome b5-like Heme/Steroid binding domain	This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors such as Swiss:O00264 [1,2]. Many members of this subfamily are membrane a ...	This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors such as Swiss:O00264 [1,2]. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	CYTOCHROME B2	oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor oxidoreductase activity L-lactate dehydrogenase activity oxidoreductase activity, acting on CH-OH group of donors L-lactate dehydrogenase (cytochrome) activity lactate dehydrogenase activity catalytic activity binding tetrapyrrole binding heme binding cation binding ion binding metal ion binding small molecule binding	oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process organic acid metabolic process lactate metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane cytosol mitochondrial intermembrane space membrane-enclosed lumen intracellular organelle lumen organelle envelope lumen organelle lumen nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036400	Cytochrome b5-like heme/steroid binding domain superfamily	Homologous Superfamily
A, B	IPR018506	Cytochrome b5, heme-binding site	Binding Site
A, B	IPR037458	L-mandelate/L-lactate dehydrogenase, FMN-binding domain	Domain
A, B	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B	IPR000262	FMN-dependent dehydrogenase	Domain
A, B	IPR008259	FMN-dependent alpha-hydroxy acid dehydrogenase, active site	Active Site
A, B	IPR001199	Cytochrome b5-like heme/steroid binding domain	Domain
A, B	IPR037396	FMN hydroxy acid dehydrogenase domain	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.