5XMJ | pdb_00005xmj

Crystal structure of quinol:fumarate reductase from Desulfovibrio gigas

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: OPM
Membrane Protein Annotation: PDBTM

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	Fumarate reductase respiratory complex cytochrome b subunit, FrdC	8077990	4003031	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Fumarate reductase respiratory complex transmembrane subunits	8077991	3000518	SCOP2 (2022-06-29)
F [auth G]	SCOP2B Superfamily	Fumarate reductase respiratory complex transmembrane subunits	8077991	3000518	SCOP2B (2022-06-29)
I [auth K]	SCOP2B Superfamily	Fumarate reductase respiratory complex transmembrane subunits	8077991	3000518	SCOP2B (2022-06-29)
L [auth O]	SCOP2B Superfamily	Fumarate reductase respiratory complex transmembrane subunits	8077991	3000518	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)
C	UNK_F_TYPE	e5xmjC1	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: UNK_F_TYPE	ECOD (1.6)
F [auth G]	UNK_F_TYPE	e5xmjG1	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: UNK_F_TYPE	ECOD (1.6)
I [auth K]	UNK_F_TYPE	e5xmjK1	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: UNK_F_TYPE	ECOD (1.6)
L [auth O]	UNK_F_TYPE	e5xmjO1	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: UNK_F_TYPE	ECOD (1.6)
A	Succ_DH_flav_C	e5xmjA1	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	e5xmjA3	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	e5xmjA2	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)
D [auth E]	Succ_DH_flav_C	e5xmjE2	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)
D [auth E]	FAD_binding_2	e5xmjE3	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)
D [auth E]	FAD_binding_3_1st	e5xmjE1	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)
G [auth I]	Succ_DH_flav_C	e5xmjI2	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)
G [auth I]	FAD_binding_2	e5xmjI3	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)
G [auth I]	FAD_binding_3_1st	e5xmjI1	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)
J [auth M]	Succ_DH_flav_C	e5xmjM1	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)
J [auth M]	FAD_binding_2	e5xmjM2	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)
J [auth M]	FAD_binding_3_1st	e5xmjM3	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)
B	Fer4_8	e5xmjB2	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	e5xmjB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_3	ECOD (1.6)
E [auth F]	Fer4_8	e5xmjF2	A: alpha arrays	X: alpha-helical ferredoxin-like	H: alpha-helical ferredoxin (From Topology)	T: alpha-helical ferredoxin	F: Fer4_8	ECOD (1.6)
E [auth F]	Fer2_3	e5xmjF1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_3	ECOD (1.6)
H [auth J]	Fer4_8	e5xmjJ1	A: alpha arrays	X: alpha-helical ferredoxin-like	H: alpha-helical ferredoxin (From Topology)	T: alpha-helical ferredoxin	F: Fer4_8	ECOD (1.6)
H [auth J]	Fer2_3	e5xmjJ2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_3	ECOD (1.6)
K [auth N]	Fer4_8	e5xmjN2	A: alpha arrays	X: alpha-helical ferredoxin-like	H: alpha-helical ferredoxin (From Topology)	T: alpha-helical ferredoxin	F: Fer4_8	ECOD (1.6)
K [auth N]	Fer2_3	e5xmjN1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_3	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)
E [auth F]	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
E [auth F]	1.10.1060.10	Mainly Alpha	Orthogonal Bundle	Fumarate Reductase Iron-sulfur Protein	Chain B, domain 2	CATH (4.3.0)
H [auth J]	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
H [auth J]	1.10.1060.10	Mainly Alpha	Orthogonal Bundle	Fumarate Reductase Iron-sulfur Protein	Chain B, domain 2	CATH (4.3.0)
K [auth N]	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
K [auth N]	1.10.1060.10	Mainly Alpha	Orthogonal Bundle	Fumarate Reductase Iron-sulfur Protein	Chain B, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F [auth G], I [auth K], L [auth O]	PF01127	Succinate dehydrogenase/Fumarate reductase transmembrane subunit (Sdh_cyt)	Succinate dehydrogenase/Fumarate reductase transmembrane subunit	-	Family
A, D [auth E], G [auth I], J [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, D [auth E], G [auth I], J [auth M]	PF00890	FAD binding domain (FAD_binding_2)	FAD binding domain	-	Family
B, E [auth F], H [auth J], K [auth N]	PF13183	4Fe-4S dicluster domain (Fer4_8)	4Fe-4S dicluster domain	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contai ...	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.	Domain
B, E [auth F], H [auth J], K [auth N]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F [auth G], I [auth K], L [auth O]	fumarate reductase respiratory complex	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 primary metabolic process metabolic process cellular process generation of precursor metabolites and energy	cellular anatomical structure membrane
A, D [auth E], G [auth I], J [auth M]	fumarate reductase 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 electron transfer activity	electron transport chain metabolic process cellular process generation of precursor metabolites and energy cellular respiration energy derivation by oxidation of organic compounds anaerobic respiration	cell periphery cellular anatomical structure plasma membrane membrane
B, E [auth F], H [auth J], K [auth N]	Succinate dehydrogenase iron-sulfur subunit	oxidoreductase activity catalytic activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding 3 iron, 4 sulfur cluster binding 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 respiratory electron transport chain electron transport chain	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F [auth G], I [auth K], L [auth O]	IPR034804	Fumarate reductase/succinate dehydrogenase, transmembrane subunit	Homologous Superfamily
C, F [auth G], I [auth K], L [auth O]	IPR000701	Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit	Family
C, F [auth G], I [auth K], L [auth O]	IPR004224	Fumarate reductase type B, transmembrane subunit	Family
A, D [auth E], G [auth I], J [auth M]	IPR003953	FAD-dependent oxidoreductase 2, FAD-binding domain	Domain
A, D [auth E], G [auth I], J [auth M]	IPR015939	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal	Domain
A, D [auth E], G [auth I], J [auth M]	IPR003952	Fumarate reductase/succinate dehydrogenase, FAD-binding site	Binding Site
A, D [auth E], G [auth I], J [auth M]	IPR037099	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily	Homologous Superfamily
A, D [auth E], G [auth I], J [auth M]	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, D [auth E], G [auth I], J [auth M]	IPR030664	FAD-dependent oxidoreductase SdhA/FrdA/AprA	Family
A, D [auth E], G [auth I], J [auth M]	IPR027477	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily	Homologous Superfamily
A, D [auth E], G [auth I], J [auth M]	IPR014006	Succinate dehydrogenase/fumarate reductase, flavoprotein subunit	Family
B, E [auth F], H [auth J], K [auth N]	IPR025192	Succinate dehydogenase/fumarate reductase N-terminal	Domain
B, E [auth F], H [auth J], K [auth N]	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
B, E [auth F], H [auth J], K [auth N]	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
B, E [auth F], H [auth J], K [auth N]	IPR006058	2Fe-2S ferredoxin, iron-sulphur binding site	Binding Site
B, E [auth F], H [auth J], K [auth N]	IPR004489	Succinate dehydrogenase/fumarate reductase iron-sulphur protein	Family
B, E [auth F], H [auth J], K [auth N]	IPR009051	Alpha-helical ferredoxin	Homologous Superfamily
B, E [auth F], H [auth J], K [auth N]	IPR050573	Succinate Dehydrogenase/Fumarate Reductase Iron-Sulfur	Family
B, E [auth F], H [auth J], K [auth N]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
B, E [auth F], H [auth J], K [auth N]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B, E [auth F], H [auth J], K [auth N]	IPR012675	Beta-grasp domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, C, D [auth E], F [auth G], G [auth I] A, C, D [auth E], F [auth G], G [auth I], I [auth K], J [auth M], L [auth O]	OPM	Transmembrane	Alpha-helical polytopic	Electron transport chain complex II superfamily	Succinate dehydrogenase/fumarate reductase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, C, D [auth E], F [auth G], G [auth I] A, C, D [auth E], F [auth G], G [auth I], I [auth K], J [auth M], L [auth O]	PDBTM	Annotated as membrane protein by PDBTM