1YQ4

Avian respiratory complex ii with 3-nitropropionate and ubiquinone

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1yq4b2	All alpha proteins	Globin-like	alpha-helical ferredoxin	Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain	Succinate dehydogenase	(Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)
B	d1yq4b1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin domains from multidomain proteins	Succinate dehydogenase iron-sulfur protein, N-terminal domain	(Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)
C	d1yq4c_	Membrane and cell surface proteins and peptides	Heme-binding four-helical bundle	Fumarate reductase respiratory complex transmembrane subunits	Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD)	automated matches	(Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)
D	d1yq4d_	Membrane and cell surface proteins and peptides	Heme-binding four-helical bundle	Fumarate reductase respiratory complex transmembrane subunits	Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD)	automated matches	(Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Fer4_8	e1yq4B1	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	e1yq4B2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_3	ECOD (1.6)
A	Succ_DH_flav_C	e1yq4A5	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	e1yq4A1	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	e1yq4A4	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)
C	Sdh_cyt	e1yq4C1	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)
D	CybS	e1yq4D1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
C	1.20.5.540	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	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	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	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	PF00890	FAD binding domain (FAD_binding_2)	FAD binding domain	-	Family
C	PF01127	Succinate dehydrogenase/Fumarate reductase transmembrane subunit (Sdh_cyt)	Succinate dehydrogenase/Fumarate reductase transmembrane subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	succinate dehydrogenase Ip subunit	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding quinone binding ubiquinone 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 iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding quinone binding ubiquinone 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 metabolic process cellular process primary metabolic process generation of precursor metabolites and energy respiratory electron transport chain electron transport chain	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 mitochondrial envelope organelle 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 mitochondrial envelope organelle cytoplasm organelle membrane respiratory chain complex protein-containing complex catalytic complex respiratory chain complex II (succinate dehydrogenase) membrane protein complex oxidoreductase complex
A	Succinate dehydrogenase flavoprotein subunit	flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound 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 flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound 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 metabolic process cellular process primary metabolic 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 metabolic process cellular process primary metabolic 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 succinate metabolic process oxoacid metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process small molecule metabolic process organic acid metabolic process	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 mitochondrial envelope organelle 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 mitochondrial envelope organelle cytoplasm organelle membrane respiratory chain complex protein-containing complex catalytic complex respiratory chain complex II (succinate dehydrogenase) membrane protein complex oxidoreductase complex
C	SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT	electron transfer activity cation binding ion binding binding metal ion binding small molecule binding	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds metabolic process cellular process primary metabolic process generation of precursor metabolites and energy	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane
D	SUCCINATE DEHYDROGENASE CYTOCHROME B, SMALL SUBUNIT	binding quinone binding ubiquinone binding small molecule binding organic cyclic compound 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 metabolic process cellular process primary metabolic 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 metabolic process cellular process primary metabolic 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 mitochondrial envelope organelle 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 mitochondrial envelope organelle cytoplasm 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
B	IPR025192	Succinate dehydogenase/fumarate reductase N-terminal	Domain
B	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
B	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
B	IPR006058	2Fe-2S ferredoxin, iron-sulphur binding site	Binding Site
B	IPR004489	Succinate dehydrogenase/fumarate reductase iron-sulphur protein	Family
B	IPR009051	Alpha-helical ferredoxin	Homologous Superfamily
B	IPR050573	Succinate Dehydrogenase/Fumarate Reductase Iron-Sulfur	Family
B	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
B	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B	IPR012675	Beta-grasp domain superfamily	Homologous Superfamily
A	IPR015939	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal	Domain
A	IPR003952	Fumarate reductase/succinate dehydrogenase, FAD-binding site	Binding Site
A	IPR037099	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily	Homologous Superfamily
A	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR003953	FAD-dependent oxidoreductase 2, FAD binding domain	Domain
A	IPR030664	FAD-dependent oxidoreductase SdhA/FrdA/AprA	Family
A	IPR027477	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily	Homologous Superfamily
A	IPR014006	Succinate dehydrogenase/fumarate reductase, flavoprotein subunit	Family
A	IPR011281	Succinate dehydrogenase, flavoprotein subunit	Family
C	IPR018495	Succinate dehydrogenase, cytochrome b subunit, conserved site	Conserved Site
C	IPR034804	Fumarate reductase/succinate dehydrogenase, transmembrane subunit	Homologous Superfamily
C	IPR000701	Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit	Family
C	IPR014314	Succinate dehydrogenase, cytochrome b556 subunit	Family
D	IPR034804	Fumarate reductase/succinate dehydrogenase, transmembrane subunit	Homologous Superfamily
D	IPR007992	Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex II	Succinate:ubiquinone oxidoreductase (SQR, Complex II; chicken heart) w. carboxin inhibitor

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	succinate dehydrogenase (ubiquinone) M-CSA #294	succinate dehydrogenase is a flavoprotein complex containing iron-sulfur centres. The enzyme is found in the inner mitochondrial membrane in eukaryotes and the plasma membrane of many aerobic or facultative bacteria. It catalyses succinate oxidation in the citric acid cycle and transfers the electrons to quinones in the membrane, thus constituting a part of the aerobic respiratory chain (known as complex II). In vivo the enzyme uses the quinone found in the organism - eukaryotic enzymes utilize ubiquinone, bacterial enzymes utilise ubiquinone or menaquinone, and archaebacterial enzymes from the Sulfolobus genus use caldariellaquinone.	Defined by 8 residues: PHE:A-130GLN:A-251HIS:A-253LEU:A-263GLU:A-266ARG:A-297HIS:A-364ARG:A-408 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.3.5.1 (PDB Primary Data) Search M-CSA Motif + EC 1.3.5.1 EC: 1.1.5 (UniProt) Search M-CSA Motif + EC 1.1.5