3KS0

Crystal structure of the heme domain of flavocytochrome b2 in complex with Fab B2B4

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
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 [auth L]	d3ks0l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth J]	d3ks0j1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d3ks0h_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth K]	d3ks0k_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth A]	d3ks0a_	Alpha and beta proteins (a+b)	Cytochrome b5-like heme/steroid binding domain	Cytochrome b5-like heme/steroid binding domain	automated matches	automated matches	yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F [auth B]	d3ks0b_	Alpha and beta proteins (a+b)	Cytochrome b5-like heme/steroid binding domain	Cytochrome b5-like heme/steroid binding domain	automated matches	automated matches	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)
C [auth A]	SCOP2B Superfamily	Cytochrome b5-like heme/steroid binding domain	8003822	3000073	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Cytochrome b5-like heme/steroid binding domain	8003822	3000073	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 [auth L]	C1-set	e3ks0L2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
A [auth L]	V-set_3	e3ks0L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
D [auth J]	C1-set	e3ks0J2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
D [auth J]	V-set_3	e3ks0J1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
B [auth H]	V-set_8	e3ks0H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B [auth H]	C1-set_1	e3ks0H2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
E [auth K]	V-set_8	e3ks0K1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
E [auth K]	C1-set_1	e3ks0K2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C [auth A]	Cyt-b5	e3ks0A1	A: a+b two layers	X: Cystatin-like	H: Cytochrome b5-like heme/steroid binding domain (From Topology)	T: Cytochrome b5-like heme/steroid binding domain	F: Cyt-b5	ECOD (1.6)
F [auth B]	Cyt-b5	e3ks0B1	A: a+b two layers	X: Cystatin-like	H: Cytochrome b5-like heme/steroid binding domain (From Topology)	T: Cytochrome b5-like heme/steroid binding domain	F: Cyt-b5	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth J]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth K]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth A]	3.10.120.10	Alpha Beta	Roll	Flavocytochrome B2	Chain A, domain 1	CATH (4.3.0)
F [auth B]	3.10.120.10	Alpha Beta	Roll	Flavocytochrome B2	Chain A, domain 1	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A [auth L], D [auth J]	Fab B2B4	L-LAMBDA	Mus musculus (house mouse)	IGLV101, IGLJ101, IGLC1*01	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202415-0)
B [auth H], E [auth K]	Fab B2B4	VH-CH1	Mus musculus (house mouse)	IGHV3-802, IGHJ201, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L], D [auth J]	Light Chain	IGLV1	Lambda	cytochrome b2, mitochondrial	SAbDab (2024-04-19)
B [auth H], E [auth K]	Heavy Chain	IGHV3	-	cytochrome b2, mitochondrial	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], F [auth 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 [auth L], D [auth J]	heme domain of flavocytochrome b2	-	-	-
B [auth H], E [auth K]	Fragment Antigen Binding B2B4	-	-	-
C [auth A], F [auth B]	Cytochrome b2, mitochondrial	oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor oxidoreductase activity oxidoreductase activity, acting on CH-OH group of donors L-lactate dehydrogenase (cytochrome) activity lactate dehydrogenase activity catalytic activity binding organic cyclic compound binding tetrapyrrole binding heme binding cation binding ion binding metal ion binding small molecule binding	oxoacid metabolic process organic hydroxy compound metabolic process cellular metabolic process carboxylic acid metabolic process organic acid metabolic process lactate metabolic process organic substance metabolic process metabolic process small molecule metabolic process cellular process monocarboxylic acid metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane respirasome 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
C [auth A], F [auth B]	IPR036400	Cytochrome b5-like heme/steroid binding domain superfamily	Homologous Superfamily
C [auth A], F [auth B]	IPR018506	Cytochrome b5, heme-binding site	Binding Site
C [auth A], F [auth B]	IPR037458	L-mandelate/L-lactate dehydrogenase, FMN-binding domain	Domain
C [auth A], F [auth B]	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
C [auth A], F [auth B]	IPR000262	FMN-dependent dehydrogenase	Domain
C [auth A], F [auth B]	IPR008259	FMN-dependent alpha-hydroxy acid dehydrogenase, active site	Active Site
C [auth A], F [auth B]	IPR001199	Cytochrome b5-like heme/steroid binding domain	Domain
C [auth A], F [auth B]	IPR037396	FMN hydroxy acid dehydrogenase domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.