6LUM | pdb_00006lum

Structure of Mycobacterium smegmatis succinate dehydrogenase 2

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: OPM
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)
E [auth B]	d6lumb2	All alpha proteins	Globin-like	alpha-helical ferredoxin	automated matches	automated matches	(Mycolicibacterium smegmatis MC2 51 ) [TaxId: 1445611 ],	SCOPe (2.08)
E [auth B]	d6lumb1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	automated matches	automated matches	(Mycolicibacterium smegmatis MC2 51 ) [TaxId: 1445611 ],	SCOPe (2.08)
J [auth K]	d6lumk2	All alpha proteins	Globin-like	alpha-helical ferredoxin	automated matches	automated matches	(Mycolicibacterium smegmatis MC2 51 ) [TaxId: 1445611 ],	SCOPe (2.08)
J [auth K]	d6lumk1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	automated matches	automated matches	(Mycolicibacterium smegmatis MC2 51 ) [TaxId: 1445611 ],	SCOPe (2.08)
O [auth Q]	d6lumq2	All alpha proteins	Globin-like	alpha-helical ferredoxin	automated matches	automated matches	(Mycolicibacterium smegmatis MC2 51 ) [TaxId: 1445611 ],	SCOPe (2.08)
O [auth Q]	d6lumq1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	automated matches	automated matches	(Mycolicibacterium smegmatis MC2 51 ) [TaxId: 1445611 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E [auth B]	Fer2_3	e6lumB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Fer2_3	ECOD (v294.1)
E [auth B]	V-set,Mst1_SARAH	e6lumB2	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: V-set,Mst1_SARAH	ECOD (v294.1)
J [auth K]	V-set,Mst1_SARAH	e6lumK1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: V-set,Mst1_SARAH	ECOD (v294.1)
O [auth Q]	V-set,Mst1_SARAH	e6lumQ1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: V-set,Mst1_SARAH	ECOD (v294.1)
D [auth A]	Fer2_3	e6lumA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Fer2_3	ECOD (v294.1)
N [auth P]	Fer2_3	e6lumP1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Fer2_3	ECOD (v294.1)
B [auth D]	Fer2_3	e6lumD1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Fer2_3	ECOD (v294.1)
G [auth H]	Fer2_3	e6lumH1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Fer2_3	ECOD (v294.1)
L [auth N]	Fer2_3	e6lumN1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Fer2_3	ECOD (v294.1)
A [auth C]	Fer2_3	e6lumC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Fer2_3	ECOD (v294.1)
K [auth M]	Fer2_3	e6lumM1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Fer2_3	ECOD (v294.1)
F [auth G]	Fer2_3	e6lumG1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Fer2_3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth B]	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (utative)
E [auth B]	1.10.1060.10	Mainly Alpha	Orthogonal Bundle	Fumarate Reductase Iron-sulfur Protein	Chain B, domain 2	CATH (utative)
J [auth K]	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (utative)
J [auth K]	1.10.1060.10	Mainly Alpha	Orthogonal Bundle	Fumarate Reductase Iron-sulfur Protein	Chain B, domain 2	CATH (utative)
O [auth Q]	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (utative)
O [auth Q]	1.10.1060.10	Mainly Alpha	Orthogonal Bundle	Fumarate Reductase Iron-sulfur Protein	Chain B, domain 2	CATH (utative)
B [auth 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 (utative)
A [auth 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 (utative)
K [auth M]	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 (utative)
F [auth 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 (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth B], J [auth K], O [auth Q]	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
E [auth B], J [auth K], O [auth Q]	PF13237	4Fe-4S dicluster domain (Fer4_10)	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
D [auth A], I [auth J], N [auth P]	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
D [auth A], I [auth J], N [auth P]	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
B [auth D], G [auth H], L [auth N]	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
E [auth B], J [auth K], O [auth Q]	Succinate dehydrogenase subunit B	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 respiratory electron transport chain electron transport chain	cell periphery cellular anatomical structure plasma membrane membrane
D [auth A], I [auth J], N [auth P]	Succinate dehydrogenase subunit A	flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding steroid dehydrogenase activity oxidoreductase activity steroid dehydrogenase activity, acting on the CH-CH group of donors oxidoreductase activity, acting on the CH-CH group of donors catalytic activity succinate dehydrogenase activity flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding steroid dehydrogenase activity oxidoreductase activity steroid dehydrogenase activity, acting on the CH-CH group of donors oxidoreductase activity, acting on the CH-CH group of donors catalytic activity succinate dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor succinate dehydrogenase (quinone) activity electron transfer activity	electron transport chain metabolic process cellular process generation of precursor metabolites and energy aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process anaerobic respiration	cell periphery cellular anatomical structure plasma membrane membrane
C [auth E], H [auth I], M [auth O]	Succinate dehydrogenase subunit F	-	-	-
B [auth D], G [auth H], L [auth N]	Succinate dehydrogenase subunit D	cation binding ion binding binding metal ion binding small molecule binding	-	cellular anatomical structure membrane
A [auth C], F [auth G], K [auth M]	Succinate dehydrogenase subunit C	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 primary metabolic process metabolic process cellular process generation of precursor metabolites and energy	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth B], J [auth K], O [auth Q]	IPR025192	Succinate dehydogenase/fumarate reductase N-terminal	Domain
E [auth B], J [auth K], O [auth Q]	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
E [auth B], J [auth K], O [auth Q]	IPR004489	Succinate dehydrogenase/fumarate reductase iron-sulphur protein	Family
E [auth B], J [auth K], O [auth Q]	IPR009051	Alpha-helical ferredoxin	Homologous Superfamily
E [auth B], J [auth K], O [auth Q]	IPR050573	Succinate Dehydrogenase/Fumarate Reductase Iron-Sulfur	Family
E [auth B], J [auth K], O [auth Q]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
E [auth B], J [auth K], O [auth Q]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
E [auth B], J [auth K], O [auth Q]	IPR012675	Beta-grasp domain superfamily	Homologous Superfamily
D [auth A], I [auth J], N [auth P]	IPR003953	FAD-dependent oxidoreductase 2, FAD-binding domain	Domain
D [auth A], I [auth J], N [auth P]	IPR015939	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal	Domain
D [auth A], I [auth J], N [auth P]	IPR003952	Fumarate reductase/succinate dehydrogenase, FAD-binding site	Binding Site
D [auth A], I [auth J], N [auth P]	IPR037099	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily	Homologous Superfamily
D [auth A], I [auth J], N [auth P]	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
D [auth A], I [auth J], N [auth P]	IPR030664	FAD-dependent oxidoreductase SdhA/FrdA/AprA	Family
D [auth A], I [auth J], N [auth P]	IPR027477	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily	Homologous Superfamily
D [auth A], I [auth J], N [auth P]	IPR014006	Succinate dehydrogenase/fumarate reductase, flavoprotein subunit	Family
D [auth A], I [auth J], N [auth P]	IPR011281	Succinate dehydrogenase, flavoprotein subunit	Family
B [auth D], G [auth H], L [auth N]	IPR034804	Fumarate reductase/succinate dehydrogenase, transmembrane subunit	Homologous Superfamily
B [auth D], G [auth H], L [auth N]	IPR000701	Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit	Family
A [auth C], F [auth G], K [auth M]	IPR039023	Succinate dehydrogenase membrane subunit SdhC, prokaryotes	Family
A [auth C], F [auth G], K [auth M]	IPR034804	Fumarate reductase/succinate dehydrogenase, transmembrane subunit	Homologous Superfamily
A [auth C], F [auth G], K [auth M]	IPR000701	Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit	Family
A [auth C], F [auth G], K [auth M]	IPR014314	Succinate dehydrogenase, cytochrome b556 subunit	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth C], B [auth D], C [auth E], D [auth A], F [auth G] A [auth C], B [auth D], C [auth E], D [auth A], F [auth G], G [auth H], H [auth I], I [auth J], K [auth M], L [auth N], M [auth O], N [auth P]	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 [auth C], B [auth D], C [auth E], D [auth A], F [auth G] A [auth C], B [auth D], C [auth E], D [auth A], F [auth G], G [auth H], H [auth I], I [auth J], K [auth M], L [auth N], M [auth O], N [auth P]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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