Annotations: 1KQG

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1kqga1	All beta proteins	Double psi beta-barrel	ADC-like	Formate dehydrogenase/DMSO reductase, C-terminal domain	Formate dehydrogenase N, alpha subunit	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1kqga2	Alpha and beta proteins (a/b)	Formate dehydrogenase/DMSO reductase, domains 1-3	Formate dehydrogenase/DMSO reductase, domains 1-3	Formate dehydrogenase/DMSO reductase, domains 1-3	Formate dehydrogenase N, alpha subunit	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1kqgb1	Alpha and beta proteins (a+b)	Ferredoxin-like	4Fe-4S ferredoxins	Ferredoxin domains from multidomain proteins	Formate dehydrogenase N, iron-sulfur (beta) subunit	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1kqgb2	Membrane and cell surface proteins and peptides	Single transmembrane helix	Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor	Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor	Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1kqgc_	Membrane and cell surface proteins and peptides	Heme-binding four-helical bundle	Transmembrane di-heme cytochromes	Formate dehydrogenase N, cytochrome (gamma) subunit	Formate dehydrogenase N, cytochrome (gamma) subunit	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	ADC-like	8040567	3001132	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Formate dehydrogenase/DMSO reductase domains 1-3	8040570	3001453	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Iron-sulfur subunit of formate dehydrogenase N transmembrane anchor	8042133	3000911	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	4Fe-4S ferredoxins	8042132	3000020	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Transmembrane di-heme cytochromes	8040572	3000517	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)
A	PF01568	e1kqgA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: PF01568	ECOD (1.6)
A	PF04879	e1kqgA3	A: a+b two layers	X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domain 1	F: PF04879	ECOD (1.6)
A	PF00384	e1kqgA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: PF00384	ECOD (1.6)
B	PF12838	e1kqgB2	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: PF12838	ECOD (1.6)
B	PF13247	e1kqgB3	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: PF13247	ECOD (1.6)
B	PF09163	e1kqgB1	A: extended segments	X: Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor (From Topology)	H: Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor (From Topology)	T: Iron-sulfur subunit of formate dehydrogenase N, transmembrane anchor	F: PF09163	ECOD (1.6)
C	PF01292	e1kqgC1	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Transmembrane di-heme cytochromes	F: PF01292	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.740	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.40.228.10	Alpha Beta	3-Layer(aba) Sandwich	Dimethylsulfoxide Reductase	domain 2	CATH (4.3.0)
A	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
B	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	1.20.5.480	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	1.20.950.20	Mainly Alpha	Up-down Bundle	Fumarate Reductase Cytochrome B subunit	Transmembrane di-heme cytochromes, Chain C	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01568	Molydopterin dinucleotide binding domain (Molydop_binding)	Molydopterin dinucleotide binding domain	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entir ...	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor [1]. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [2].	Domain
A	PF04879	Molybdopterin oxidoreductase Fe4S4 domain (Molybdop_Fe4S4)	Molybdopterin oxidoreductase Fe4S4 domain	This domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of PDB:1aa6 is an Fe4S4 cluster just below the protein surface [1].	Domain
A	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase	-	Family
B	PF12838	4Fe-4S dicluster domain (Fer4_7)	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	PF09163	Formate dehydrogenase N, transmembrane (Form-deh_trans)	Formate dehydrogenase N, transmembrane	Members of this family are predominantly found in the beta subunit of formate dehydrogenase, and consist of a single transmembrane helix. They act as a transmembrane anchor, and allow for conduction of electrons within the protein [1].	Domain
B	PF00037	4Fe-4S binding domain (Fer4)	4Fe-4S binding 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
C	PF01292	Prokaryotic cytochrome b561 (Ni_hydr_CYTB)	Prokaryotic cytochrome b561	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT	oxidoreductase activity, acting on CH or CH2 groups, quinone or similar compound as acceptor oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups formate dehydrogenase (quinone) activity catalytic activity cation binding transition metal ion binding molybdenum ion binding ion binding binding metal ion binding small molecule binding organic cyclic compound binding molybdopterin cofactor binding oxidoreductase activity, acting on CH or CH2 groups, quinone or similar compound as acceptor oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups formate dehydrogenase (quinone) activity catalytic activity cation binding transition metal ion binding molybdenum ion binding ion binding binding metal ion binding small molecule binding organic cyclic compound binding molybdopterin cofactor binding oxidoreductase activity, acting on the aldehyde or oxo group of donors, cytochrome as acceptor formate dehydrogenase (cytochrome-c-553) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding formate dehydrogenase (NAD+) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor electron transfer activity selenium binding	organonitrogen compound catabolic process heme metabolic process pigment metabolic process organonitrogen compound metabolic process catabolic process heme oxidation tetrapyrrole metabolic process organic cyclic compound catabolic process organic cyclic compound metabolic process organic substance metabolic process porphyrin-containing compound catabolic process metabolic process porphyrin-containing compound metabolic process organic substance catabolic process organonitrogen compound catabolic process heme metabolic process pigment metabolic process organonitrogen compound metabolic process catabolic process heme oxidation tetrapyrrole metabolic process organic cyclic compound catabolic process organic cyclic compound metabolic process organic substance metabolic process porphyrin-containing compound catabolic process metabolic process porphyrin-containing compound metabolic process organic substance catabolic process tetrapyrrole catabolic process anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process respiratory electron transport chain electron transport chain cellular process generation of precursor metabolites and energy anaerobic respiration oxoacid metabolic process formate oxidation carboxylic acid metabolic process organic acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process formate metabolic process	membrane cellular anatomical entity protein-containing complex catalytic complex formate dehydrogenase complex oxidoreductase complex outer membrane-bounded periplasmic space cell envelope periplasmic space
B	FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT	oxidoreductase activity, acting on CH or CH2 groups, quinone or similar compound as acceptor oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups formate dehydrogenase (quinone) activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding electron transfer activity cation binding ion binding metal ion binding	organonitrogen compound catabolic process heme metabolic process pigment metabolic process organonitrogen compound metabolic process catabolic process heme oxidation tetrapyrrole metabolic process organic cyclic compound catabolic process organic cyclic compound metabolic process organic substance metabolic process porphyrin-containing compound catabolic process metabolic process porphyrin-containing compound metabolic process organic substance catabolic process organonitrogen compound catabolic process heme metabolic process pigment metabolic process organonitrogen compound metabolic process catabolic process heme oxidation tetrapyrrole metabolic process organic cyclic compound catabolic process organic cyclic compound metabolic process organic substance metabolic process porphyrin-containing compound catabolic process metabolic process porphyrin-containing compound metabolic process organic substance catabolic process tetrapyrrole catabolic process anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process respiratory electron transport chain electron transport chain cellular process generation of precursor metabolites and energy anaerobic respiration oxoacid metabolic process formate oxidation carboxylic acid metabolic process organic acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process formate metabolic process	membrane cellular anatomical entity cell periphery plasma membrane protein-containing complex catalytic complex formate dehydrogenase complex oxidoreductase complex
C	FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556(FDN) SUBUNIT	oxidoreductase activity, acting on CH or CH2 groups, quinone or similar compound as acceptor oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups formate dehydrogenase (quinone) activity catalytic activity binding organic cyclic compound binding tetrapyrrole binding heme binding formate dehydrogenase (NAD+) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor electron transfer activity cation binding oxidoreductase activity, acting on CH or CH2 groups, quinone or similar compound as acceptor oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups formate dehydrogenase (quinone) activity catalytic activity binding organic cyclic compound binding tetrapyrrole binding heme binding formate dehydrogenase (NAD+) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor electron transfer activity cation binding ion binding metal ion binding small molecule binding	organonitrogen compound catabolic process heme metabolic process pigment metabolic process organonitrogen compound metabolic process catabolic process heme oxidation tetrapyrrole metabolic process organic cyclic compound catabolic process organic cyclic compound metabolic process organic substance metabolic process porphyrin-containing compound catabolic process metabolic process porphyrin-containing compound metabolic process organic substance catabolic process organonitrogen compound catabolic process heme metabolic process pigment metabolic process organonitrogen compound metabolic process catabolic process heme oxidation tetrapyrrole metabolic process organic cyclic compound catabolic process organic cyclic compound metabolic process organic substance metabolic process porphyrin-containing compound catabolic process metabolic process porphyrin-containing compound metabolic process organic substance catabolic process tetrapyrrole catabolic process anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process respiratory electron transport chain electron transport chain cellular process generation of precursor metabolites and energy anaerobic respiration oxoacid metabolic process formate oxidation carboxylic acid metabolic process organic acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process formate metabolic process	membrane cellular anatomical entity cell periphery plasma membrane protein-containing complex catalytic complex formate dehydrogenase complex oxidoreductase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
A	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
A	IPR006656	Molybdopterin oxidoreductase	Domain
A	IPR006443	Formate dehydrogenase-N, alpha subunit	Family
A	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A	IPR006655	Molybdopterin oxidoreductase, prokaryotic, conserved site	Conserved Site
A	IPR027467	Molybdopterin oxidoreductase, molybdopterin cofactor binding site	Binding Site
B	IPR015246	Formate dehydrogenase, transmembrane	Domain
B	IPR038384	Formate dehydrogenase, C-terminal domain superfamily	Homologous Superfamily
B	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
B	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B	IPR006470	Formate dehydrogenase iron-sulphur subunit, Proteobacteria	Family
B	IPR014603	Formate dehydrogenase iron-sulphur subunit	Family
C	IPR011577	Cytochrome b561, bacterial/Ni-hydrogenase	Domain
C	IPR006471	Formate dehydrogenase, gamma subunit	Family
C	IPR016174	Di-haem cytochrome, transmembrane	Homologous Superfamily

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex II	Formate dehydrogenase-N

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 R01GM133198.