3VRB | pdb_00003vrb

Mitochondrial rhodoquinol-fumarate reductase from the parasitic nematode Ascaris suum with the specific inhibitor flutolanil and substrate fumarate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d3vrbf2	All alpha proteins	Globin-like	alpha-helical ferredoxin	automated matches	automated matches	(Ascaris suum ) [TaxId: 6253 ],	SCOPe (2.08)
F	d3vrbf1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	automated matches	automated matches	(Ascaris suum ) [TaxId: 6253 ],	SCOPe (2.08)
B	d3vrbb2	All alpha proteins	Globin-like	alpha-helical ferredoxin	automated matches	automated matches	(Ascaris suum ) [TaxId: 6253 ],	SCOPe (2.08)
B	d3vrbb1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	automated matches	automated matches	(Ascaris suum ) [TaxId: 6253 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	CybS	e3vrbH2	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Fumarate reductase respiratory complex transmembrane subunits	F: CybS	ECOD (1.6)
D	CybS	e3vrbD2	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Fumarate reductase respiratory complex transmembrane subunits	F: CybS	ECOD (1.6)
G	Sdh_cyt	e3vrbG2	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Fumarate reductase respiratory complex transmembrane subunits	F: Sdh_cyt	ECOD (1.6)
C	Sdh_cyt	e3vrbC2	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Fumarate reductase respiratory complex transmembrane subunits	F: Sdh_cyt	ECOD (1.6)
F	Fer4_8	e3vrbF5	A: alpha arrays	X: alpha-helical ferredoxin-like	H: alpha-helical ferredoxin (From Topology)	T: alpha-helical ferredoxin	F: Fer4_8	ECOD (1.6)
F	Fer2_3	e3vrbF6	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_3	ECOD (1.6)
B	Fer4_8	e3vrbB5	A: alpha arrays	X: alpha-helical ferredoxin-like	H: alpha-helical ferredoxin (From Topology)	T: alpha-helical ferredoxin	F: Fer4_8	ECOD (1.6)
B	Fer2_3	e3vrbB6	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_3	ECOD (1.6)
E	Succ_DH_flav_C	e3vrbE2	A: alpha bundles	X: Spectrin repeat-like	H: Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain (From Topology)	T: Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	F: Succ_DH_flav_C	ECOD (1.6)
E	FAD_binding_2	e3vrbE1	A: a+b complex topology	X: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain (From Topology)	H: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain (From Topology)	T: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	F: FAD_binding_2	ECOD (1.6)
E	FAD_binding_3_1st	e3vrbE3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: FAD_binding_3_1st	ECOD (1.6)
A	Succ_DH_flav_C	e3vrbA1	A: alpha bundles	X: Spectrin repeat-like	H: Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain (From Topology)	T: Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	F: Succ_DH_flav_C	ECOD (1.6)
A	FAD_binding_2	e3vrbA3	A: a+b complex topology	X: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain (From Topology)	H: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain (From Topology)	T: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	F: FAD_binding_2	ECOD (1.6)
A	FAD_binding_3_1st	e3vrbA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: FAD_binding_3_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	1.20.1300.10	Mainly Alpha	Up-down Bundle	3 helical TM bundles of succinate and fumarate reductases	Fumarate reductase/succinate dehydrogenase, transmembrane subunit	CATH (4.3.0)
D	1.20.1300.10	Mainly Alpha	Up-down Bundle	3 helical TM bundles of succinate and fumarate reductases	Fumarate reductase/succinate dehydrogenase, transmembrane subunit	CATH (4.3.0)
G	1.20.1300.10	Mainly Alpha	Up-down Bundle	3 helical TM bundles of succinate and fumarate reductases	Fumarate reductase/succinate dehydrogenase, transmembrane subunit	CATH (4.3.0)
C	1.20.1300.10	Mainly Alpha	Up-down Bundle	3 helical TM bundles of succinate and fumarate reductases	Fumarate reductase/succinate dehydrogenase, transmembrane subunit	CATH (4.3.0)
F	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
F	1.10.1060.10	Mainly Alpha	Orthogonal Bundle	Fumarate Reductase Iron-sulfur Protein	Chain B, domain 2	CATH (4.3.0)
B	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
B	1.10.1060.10	Mainly Alpha	Orthogonal Bundle	Fumarate Reductase Iron-sulfur Protein	Chain B, domain 2	CATH (4.3.0)
E	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
E	3.90.700.10	Alpha Beta	Alpha-Beta Complex	Flavocytochrome C3	Chain A, domain 1	CATH (4.3.0)
E	1.20.58.100	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
E	4.10.80.40	Few Secondary Structures	Irregular	Rhinovirus 14, subunit 4	succinate dehydrogenase protein domain	CATH (4.3.0)
A	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
A	3.90.700.10	Alpha Beta	Alpha-Beta Complex	Flavocytochrome C3	Chain A, domain 1	CATH (4.3.0)
A	1.20.58.100	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
A	4.10.80.40	Few Secondary Structures	Irregular	Rhinovirus 14, subunit 4	succinate dehydrogenase protein domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D, H	PF05328	CybS, succinate dehydrogenase cytochrome B small subunit (CybS)	CybS, succinate dehydrogenase cytochrome B small subunit	-	Family
C, G	PF01127	Succinate dehydrogenase/Fumarate reductase transmembrane subunit (Sdh_cyt)	Succinate dehydrogenase/Fumarate reductase transmembrane subunit	-	Family
B, F	PF13085	2Fe-2S iron-sulfur cluster binding domain (Fer2_3)	2Fe-2S iron-sulfur cluster binding domain	The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which abeta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated.	Domain
B, F	PF13534	4Fe-4S dicluster domain (Fer4_17)	4Fe-4S dicluster domain	This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.	Domain
A, E	PF02910	Fumarate reductase flavoprotein C-term (Succ_DH_flav_C)	Fumarate reductase flavoprotein C-term	This family contains fumarate reductases, succinate dehydrogenases and L-aspartate oxidases.	Domain
A, E	PF00890	FAD binding domain (FAD_binding_2)	FAD binding domain	This family includes members that bind FAD. This family includes the flavoprotein subunits from succinate and fumarate dehydrogenase, aspartate oxidase and the alpha subunit of adenylylsulphate reductase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, H	Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial	binding quinone binding ubiquinone binding small molecule binding tetrapyrrole binding heme binding cation binding ion binding metal ion binding	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy mitochondrial electron transport, succinate to ubiquinone aerobic electron transport chain oxidative phosphorylation ATP synthesis coupled electron transport electron transport chain respiratory electron transport chain aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy mitochondrial electron transport, succinate to ubiquinone aerobic electron transport chain oxidative phosphorylation ATP synthesis coupled electron transport electron transport chain respiratory electron transport chain mitochondrial ATP synthesis coupled electron transport	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane respiratory chain complex protein-containing complex catalytic complex respiratory chain complex II (succinate dehydrogenase) membrane protein complex oxidoreductase complex
C, G	Cytochrome b-large subunit	binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy mitochondrial electron transport, succinate to ubiquinone aerobic electron transport chain oxidative phosphorylation ATP synthesis coupled electron transport electron transport chain respiratory electron transport chain aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy mitochondrial electron transport, succinate to ubiquinone aerobic electron transport chain oxidative phosphorylation ATP synthesis coupled electron transport electron transport chain respiratory electron transport chain mitochondrial ATP synthesis coupled electron transport	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane respiratory chain complex protein-containing complex catalytic complex respiratory chain complex II (succinate dehydrogenase) membrane protein complex oxidoreductase complex
B, F	Iron-sulfur subunit of succinate dehydrogenase	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding 3 iron, 4 sulfur cluster binding oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor catalytic activity succinate dehydrogenase (quinone) activity 4 iron, 4 sulfur cluster binding electron transfer activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding 3 iron, 4 sulfur cluster binding oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor catalytic activity succinate dehydrogenase (quinone) activity 4 iron, 4 sulfur cluster binding electron transfer activity cation binding ion binding metal ion binding	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy mitochondrial electron transport, succinate to ubiquinone aerobic electron transport chain oxidative phosphorylation ATP synthesis coupled electron transport electron transport chain respiratory electron transport chain aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy mitochondrial electron transport, succinate to ubiquinone aerobic electron transport chain oxidative phosphorylation ATP synthesis coupled electron transport electron transport chain respiratory electron transport chain mitochondrial ATP synthesis coupled electron transport	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane respiratory chain complex protein-containing complex catalytic complex respiratory chain complex II (succinate dehydrogenase) membrane protein complex oxidoreductase complex
A, E	Flavoprotein subunit of complex II	flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor catalytic activity succinate dehydrogenase (quinone) activity flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor catalytic activity succinate dehydrogenase (quinone) activity electron transfer activity	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy mitochondrial electron transport, succinate to ubiquinone aerobic electron transport chain oxidative phosphorylation ATP synthesis coupled electron transport electron transport chain respiratory electron transport chain aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy mitochondrial electron transport, succinate to ubiquinone aerobic electron transport chain oxidative phosphorylation ATP synthesis coupled electron transport electron transport chain respiratory electron transport chain mitochondrial ATP synthesis coupled electron transport	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 respiratory chain complex protein-containing complex catalytic complex respiratory chain complex II (succinate dehydrogenase) membrane protein complex oxidoreductase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, H	IPR034804	Fumarate reductase/succinate dehydrogenase, transmembrane subunit	Homologous Superfamily
D, H	IPR007992	Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS	Family
C, G	IPR018495	Succinate dehydrogenase, cytochrome b subunit, conserved site	Conserved Site
C, G	IPR034804	Fumarate reductase/succinate dehydrogenase, transmembrane subunit	Homologous Superfamily
C, G	IPR000701	Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit	Family
C, G	IPR014314	Succinate dehydrogenase, cytochrome b556 subunit	Family
B, F	IPR025192	Succinate dehydogenase/fumarate reductase N-terminal	Domain
B, F	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
B, F	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
B, F	IPR006058	2Fe-2S ferredoxin, iron-sulphur binding site	Binding Site
B, F	IPR004489	Succinate dehydrogenase/fumarate reductase iron-sulphur protein	Family
B, F	IPR009051	Alpha-helical ferredoxin	Homologous Superfamily
B, F	IPR050573	Succinate Dehydrogenase/Fumarate Reductase Iron-Sulfur	Family
B, F	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
B, F	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B, F	IPR012675	Beta-grasp domain superfamily	Homologous Superfamily
A, E	IPR003953	FAD-dependent oxidoreductase 2, FAD-binding domain	Domain
A, E	IPR015939	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal	Domain
A, E	IPR003952	Fumarate reductase/succinate dehydrogenase, FAD-binding site	Binding Site
A, E	IPR037099	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily	Homologous Superfamily
A, E	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, E	IPR030664	FAD-dependent oxidoreductase SdhA/FrdA/AprA	Family
A, E	IPR027477	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily	Homologous Superfamily
A, E	IPR014006	Succinate dehydrogenase/fumarate reductase, flavoprotein subunit	Family
A, E	IPR011281	Succinate dehydrogenase, flavoprotein subunit	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G, H	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G, H	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E A, B, C, D, E, F, G, H	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Oxidoreductases	Mitochondrial rhodoquinol-fumarate reductase

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.

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Mitochondrial rhodoquinol-fumarate reductase from the parasitic nematode Ascaris suum with the specific inhibitor flutolanil and substrate fumarate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

3VRB | pdb_00003vrb