4KX6 | pdb_00004kx6

Plasticity of the quinone-binding site of the complex II homolog quinol:fumarate reductase

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
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H [auth P]	d4kx6p_	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)	Fumarate reductase subunit FrdD	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d4kx6d_	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)	Fumarate reductase subunit FrdD	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
G [auth O]	d4kx6o_	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)	Fumarate reductase subunit FrdC	(Escherichia coli DH1 ) [TaxId: 536056 ],	SCOPe (2.08)
C	d4kx6c_	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)	Fumarate reductase subunit FrdC	(Escherichia coli DH1 ) [TaxId: 536056 ],	SCOPe (2.08)
F [auth N]	d4kx6n2	All alpha proteins	Globin-like	alpha-helical ferredoxin	Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain	Fumarate reductase	(Escherichia coli BW2952 ) [TaxId: 595496 ],	SCOPe (2.08)
F [auth N]	d4kx6n1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin domains from multidomain proteins	Fumarate reductase iron-sulfur protein, N-terminal domain	(Escherichia coli BW2952 ) [TaxId: 595496 ],	SCOPe (2.08)
B	d4kx6b2	All alpha proteins	Globin-like	alpha-helical ferredoxin	Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain	Fumarate reductase	(Escherichia coli BW2952 ) [TaxId: 595496 ],	SCOPe (2.08)
B	d4kx6b1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin domains from multidomain proteins	Fumarate reductase iron-sulfur protein, N-terminal domain	(Escherichia coli BW2952 ) [TaxId: 595496 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H [auth P]	SCOP2B Superfamily	Fumarate reductase respiratory complex transmembrane subunits	8040223	3000518	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Fumarate reductase respiratory complex transmembrane subunits	8040223	3000518	SCOP2B (2022-06-29)
E [auth M]	SCOP2B Superfamily	Succinate dehydrogenase/fumarate reductase domain-like	8056076	3000054	SCOP2B (2022-06-29)
E [auth M]	SCOP2B Superfamily	L-aspartate oxidase C-terminal domain-like	8056077	3000021	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	L-aspartate oxidase C-terminal domain-like	8056077	3000021	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Succinate dehydrogenase/fumarate reductase domain-like	8056076	3000054	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)
H [auth P]	Fumarate_red_D	e4kx6P1	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: Fumarate_red_D	ECOD (1.6)
D	Fumarate_red_D	e4kx6D1	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: Fumarate_red_D	ECOD (1.6)
G [auth O]	Fumarate_red_C	e4kx6O1	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: Fumarate_red_C	ECOD (1.6)
C	Fumarate_red_C	e4kx6C1	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: Fumarate_red_C	ECOD (1.6)
F [auth N]	Fer4_8	e4kx6N1	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 [auth N]	Fer2_3	e4kx6N2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_3	ECOD (1.6)
B	Fer4_8	e4kx6B1	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	e4kx6B2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_3	ECOD (1.6)
E [auth M]	Succ_DH_flav_C	e4kx6M4	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 [auth M]	FAD_binding_2	e4kx6M2	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 [auth M]	FAD_binding_3_1st	e4kx6M3	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	e4kx6A4	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	e4kx6A2	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	e4kx6A3	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 [auth P]	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 [auth O]	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 [auth N]	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
F [auth N]	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 [auth M]	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 [auth M]	3.90.700.10	Alpha Beta	Alpha-Beta Complex	Flavocytochrome C3	Chain A, domain 1	CATH (4.3.0)
E [auth M]	1.20.58.100	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
E [auth M]	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 [auth P]	PF02313	Fumarate reductase subunit D (Fumarate_red_D)	Fumarate reductase subunit D	Fumarate reductase is a membrane-bound flavoenzyme consisting of four subunits, A-B. A and B comprise the membrane-extrinsic catalytic domain and C and D link the catalytic centres to the electron-transport chain. This family consists of the 13kD hyd ...	Fumarate reductase is a membrane-bound flavoenzyme consisting of four subunits, A-B. A and B comprise the membrane-extrinsic catalytic domain and C and D link the catalytic centres to the electron-transport chain. This family consists of the 13kD hydrophobic subunit D.	Domain
A, E [auth M]	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 [auth M]	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 [auth P]	Fumarate reductase subunit D	oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity	organelle assembly cell projection organization bacterial-type flagellum assembly membraneless organelle assembly cellular component biogenesis cellular component organization bacterial-type flagellum organization organelle organization cellular component assembly cellular process cellular component organization or biogenesis cell projection assembly anaerobic electron transport chain cellular respiration organelle assembly cell projection organization bacterial-type flagellum assembly membraneless organelle assembly cellular component biogenesis cellular component organization bacterial-type flagellum organization organelle organization cellular component assembly cellular process cellular component organization or biogenesis cell projection assembly anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process generation of precursor metabolites and energy anaerobic respiration oxoacid metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process small molecule metabolic process fumarate metabolic process organic acid metabolic process fermentation	respiratory chain complex fumarate reductase complex protein-containing complex cellular anatomical structure catalytic complex membrane membrane protein complex cell periphery plasma membrane
C, G [auth O]	Fumarate reductase subunit C	-	-	-
B, F [auth N]	Fumarate reductase (Anaerobic), Fe-S subunit	-	-	-
A, E [auth M]	Fumarate reductase flavoprotein subunit	oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity FAD binding 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 oxidoreductase activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity FAD binding 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	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process generation of precursor metabolites and energy anaerobic respiration cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process generation of precursor metabolites and energy anaerobic respiration fermentation organelle assembly cell projection organization bacterial-type flagellum assembly membraneless organelle assembly cellular component biogenesis cellular component organization bacterial-type flagellum organization organelle organization cellular component assembly cellular component organization or biogenesis cell projection assembly	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol respiratory chain complex fumarate reductase complex protein-containing complex catalytic complex membrane protein complex cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, H [auth P]	IPR034804	Fumarate reductase/succinate dehydrogenase, transmembrane subunit	Homologous Superfamily
D, H [auth P]	IPR003418	Fumarate reductase, subunit D	Family
A, E [auth M]	IPR003953	FAD-dependent oxidoreductase 2, FAD-binding domain	Domain
A, E [auth M]	IPR015939	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal	Domain
A, E [auth M]	IPR003952	Fumarate reductase/succinate dehydrogenase, FAD-binding site	Binding Site
A, E [auth M]	IPR037099	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily	Homologous Superfamily
A, E [auth M]	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, E [auth M]	IPR030664	FAD-dependent oxidoreductase SdhA/FrdA/AprA	Family
A, E [auth M]	IPR005884	Fumarate reductase, flavoprotein subunit	Family
A, E [auth M]	IPR027477	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily	Homologous Superfamily
A, E [auth M]	IPR014006	Succinate dehydrogenase/fumarate reductase, flavoprotein subunit	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, D, E [auth M], H [auth P]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, D, E [auth M], H [auth P]	MemProtMD	Annotated as membrane protein by MemProtMD

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.