2WDV | pdb_00002wdv

E. coli succinate:quinone oxidoreductase (SQR) with an empty quinone- binding pocket

External Resource: Annotation

Domain Annotation: SCOP2 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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J	SCOP2B Superfamily	alpha-helical ferredoxin	8017662	3000026	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8017659	3000113	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	alpha-helical ferredoxin	8017662	3000026	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8017659	3000113	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	alpha-helical ferredoxin	8017662	3000026	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8017659	3000113	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Fumarate reductase respiratory complex transmembrane subunits	8043768	3000518	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Fumarate reductase respiratory complex transmembrane subunits	8043768	3000518	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Fumarate reductase respiratory complex transmembrane subunits	8043768	3000518	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Fumarate reductase respiratory complex transmembrane subunits	8043765	3000518	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Fumarate reductase respiratory complex transmembrane subunits	8043765	3000518	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Fumarate reductase respiratory complex transmembrane subunits	8043765	3000518	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	L-aspartate oxidase C-terminal domain-like	8056068	3000021	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Succinate dehydrogenase/fumarate reductase domain-like	8056067	3000054	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	L-aspartate oxidase C-terminal domain-like	8056068	3000021	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Succinate dehydrogenase/fumarate reductase domain-like	8056067	3000054	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	L-aspartate oxidase C-terminal domain-like	8056068	3000021	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Succinate dehydrogenase/fumarate reductase domain-like	8056067	3000054	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J	e2wdvJ1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: HTH_3	F:	ECOD (20:10:01)
F	e2wdvF1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: HTH_3	F:	ECOD (20:10:01)
B	e2wdvB1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: HTH_3	F:	ECOD (20:10:01)
L	e2wdvL1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: HTH_3	F:	ECOD (20:10:01)
H	e2wdvH1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: HTH_3	F:	ECOD (20:10:01)
D	e2wdvD1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: HTH_3	F:	ECOD (20:10:01)
K	e2wdvK1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: HTH_3	F:	ECOD (20:10:01)
G	e2wdvG1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: HTH_3	F:	ECOD (20:10:01)
C	e2wdvC1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: HTH_3	F:	ECOD (20:10:01)
I	e2wdvI1	A: Four-helical up-and-down bundle	X: Glycosyl hydrolase domain	H: Glycosyl hydrolase domain	T: Ribosomal_S27	F:	ECOD (20:10:01)
E	e2wdvE1	A: Four-helical up-and-down bundle	X: Glycosyl hydrolase domain	H: Glycosyl hydrolase domain	T: Ribosomal_S27	F:	ECOD (20:10:01)
A	e2wdvA2	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: HTH_3	F:	ECOD (20:10:01)
A	e2wdvA4	A: RuvA-C	X: post-HMGL domain-like	H: post-HMGL domain-like	T: Acetyltransf_9	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
J	1.10.1060.10	Mainly Alpha	Orthogonal Bundle	Fumarate Reductase Iron-sulfur Protein	Chain B, domain 2	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)
L	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)
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)
K	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)
I	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
I	3.90.700.10	Alpha Beta	Alpha-Beta Complex	Flavocytochrome C3	Chain A, domain 1	CATH (4.3.0)
I	1.20.58.100	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
I	4.10.80.40	Few Secondary Structures	Irregular	Rhinovirus 14, subunit 4	succinate dehydrogenase protein domain	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
B, F, J	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, J	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, I	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, I	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
B, F, J	SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT	iron-sulfur cluster binding binding metal cluster binding small molecule binding 2 iron, 2 sulfur cluster 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 binding metal cluster binding small molecule binding 2 iron, 2 sulfur cluster 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 aerobic electron transport chain oxidative phosphorylation respiratory electron transport chain electron transport chain	cellular anatomical structure membrane respiratory chain complex protein-containing complex catalytic complex respiratory chain complex II (succinate dehydrogenase) membrane protein complex oxidoreductase complex cell periphery plasma membrane
D, H, L	SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN	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 aerobic electron transport chain oxidative phosphorylation respiratory electron transport chain electron transport chain cytochrome complex assembly cellular component organization 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 aerobic electron transport chain oxidative phosphorylation respiratory electron transport chain electron transport chain cytochrome complex assembly cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis	cellular anatomical structure membrane respiratory chain complex protein-containing complex catalytic complex respiratory chain complex II (succinate dehydrogenase) membrane protein complex oxidoreductase complex cell periphery plasma membrane
C, G, K	SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT	binding tetrapyrrole binding heme binding quinone binding ubiquinone 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 cation binding binding tetrapyrrole binding heme binding quinone binding ubiquinone 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 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 aerobic electron transport chain oxidative phosphorylation respiratory electron transport chain electron transport chain cytochrome complex assembly cellular component organization 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 aerobic electron transport chain oxidative phosphorylation respiratory electron transport chain electron transport chain cytochrome complex assembly cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis	cellular anatomical structure membrane respiratory chain complex protein-containing complex catalytic complex respiratory chain complex II (succinate dehydrogenase) membrane protein complex oxidoreductase complex cell periphery plasma membrane
A, E, I	SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT	oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor succinate dehydrogenase (quinone) activity oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor 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 aerobic electron transport chain oxidative phosphorylation respiratory electron transport chain electron transport chain anaerobic respiration	cellular anatomical structure membrane respiratory chain complex protein-containing complex catalytic complex respiratory chain complex II (succinate dehydrogenase) membrane protein complex oxidoreductase complex cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, F, J	IPR025192	Succinate dehydogenase/fumarate reductase N-terminal	Domain
B, F, J	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
B, F, J	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
B, F, J	IPR004489	Succinate dehydrogenase/fumarate reductase iron-sulphur protein	Family
B, F, J	IPR009051	Alpha-helical ferredoxin	Homologous Superfamily
B, F, J	IPR050573	Succinate Dehydrogenase/Fumarate Reductase Iron-Sulfur	Family
B, F, J	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
B, F, J	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B, F, J	IPR012675	Beta-grasp domain superfamily	Homologous Superfamily
D, H, L	IPR034804	Fumarate reductase/succinate dehydrogenase, transmembrane subunit	Homologous Superfamily
D, H, L	IPR000701	Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit	Family
D, H, L	IPR014312	Succinate dehydrogenase, hydrophobic membrane anchor	Family
C, G, K	IPR034804	Fumarate reductase/succinate dehydrogenase, transmembrane subunit	Homologous Superfamily
C, G, K	IPR014314	Succinate dehydrogenase, cytochrome b556 subunit	Family
C, G, K	IPR018495	Succinate dehydrogenase, cytochrome b subunit, conserved site	Conserved Site
C, G, K	IPR000701	Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit	Family
A, E, I	IPR003953	FAD-dependent oxidoreductase 2, FAD-binding domain	Domain
A, E, I	IPR015939	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal	Domain
A, E, I	IPR003952	Fumarate reductase/succinate dehydrogenase, FAD-binding site	Binding Site
A, E, I	IPR037099	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily	Homologous Superfamily
A, E, I	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, E, I	IPR030664	FAD-dependent oxidoreductase SdhA/FrdA/AprA	Family
A, E, I	IPR027477	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily	Homologous Superfamily
A, E, I	IPR014006	Succinate dehydrogenase/fumarate reductase, flavoprotein subunit	Family
A, E, I	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, I, J, K, L	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, I, J, K, L	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, I, J, K, L	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex II	Succinate:quinone oxidoreductase (SQR, Complex II) with carboxin in Q-site