7NZ1 | pdb_00007nz1

Respiratory complex I from Escherichia coli - focused refinement of cytoplasmic arm

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: mpstruc
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth I]	SCOP2 Family	Ferredoxin domains from multidomain proteins	8103950	4000021	SCOP2 (2022-06-29)
F [auth I]	SCOP2 Superfamily	4Fe-4S ferredoxins	8103951	3000020	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth I]	Fer4_21_1	e7nz1I1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21_1	ECOD (1.6)
D [auth F]	NADH_4Fe-4S	e7nz1F2	A: alpha bundles	X: Bromodomain-like	H: Nqo1C-terminal domain-like (From Topology)	T: Nqo1C-terminal domain-like	F: NADH_4Fe-4S	ECOD (1.6)
D [auth F]	F_UNCLASSIFIED	e7nz1F3	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Nqo1 middle domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
D [auth F]	Complex1_51K	e7nz1F1	A: a/b three-layered sandwiches	X: Nqo1 FMN-binding domain-like (From Topology)	H: Nqo1 FMN-binding domain-like (From Topology)	T: Nqo1 FMN-binding domain-like	F: Complex1_51K	ECOD (1.6)
C [auth E]	2Fe-2S_thioredx_N	e7nz1E1	A: alpha bundles	X: NQO2 helical bundle domain (From Topology)	H: NQO2 helical bundle domain (From Topology)	T: NQO2 helical bundle domain	F: 2Fe-2S_thioredx_N	ECOD (1.6)
C [auth E]	2Fe-2S_thioredx_C	e7nz1E2	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: 2Fe-2S_thioredx_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth G]	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (utative)
B [auth D]	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
F [auth I]	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
E [auth G]	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 entire s ...	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
E [auth G]	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
E [auth G]	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase		Domain
E [auth G]	PF22117	NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain (Fer4_Nqo3)	NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain	NADH-quinone oxidoreductase subunit 3 (Nqo3) is a component of respiratory complex I. This protein is located at the peripheral arm of the complex and consists of multiple domains. This entry represents the second ferredoxin-like domain which contain ...	NADH-quinone oxidoreductase subunit 3 (Nqo3) is a component of respiratory complex I. This protein is located at the peripheral arm of the complex and consists of multiple domains. This entry represents the second ferredoxin-like domain which contains Fe4-S4 cluster, one of the redox centers of the complex [1-5].	Domain
E [auth G]	PF13510	2Fe-2S iron-sulfur cluster binding domain (Fer2_4)	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 a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. Th ...	The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This cluster appears within sarcosine oxidase proteins.	Domain
E [auth G]	PF10588	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region (NADH-G_4Fe-4S_3)	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region		Domain
D [auth F]	PF01512	Nuo51 FMN-binding domain (Complex1_51K)	Nuo51 FMN-binding domain	This entry represents the FMN-binding domain of NADH-ubiquinone oxidoreductase 51kDa subunit from NADH:ubiquinone oxidoreductase.	Domain
D [auth F]	PF10589	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region (NADH_4Fe-4S)	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region		Domain
C [auth E]	PF01257	Thioredoxin-like [2Fe-2S] ferredoxin (2Fe-2S_thioredx)	Thioredoxin-like [2Fe-2S] ferredoxin	-	Family
B [auth D]	PF00329	Respiratory-chain NADH dehydrogenase, 30 Kd subunit (Complex1_30kDa)	Respiratory-chain NADH dehydrogenase, 30 Kd subunit		Domain
B [auth D]	PF00346	Respiratory-chain NADH dehydrogenase, 49 Kd subunit (Complex1_49kDa)	Respiratory-chain NADH dehydrogenase, 49 Kd subunit	-	Family
A [auth B]	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth I]	NADH-quinone oxidoreductase subunit I	oxidoreductase activity NAD(P)H dehydrogenase (quinone) activity oxidoreductase activity, acting on NAD(P)H catalytic activity oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor NADH dehydrogenase (quinone) (non-electrogenic) activity NADH dehydrogenase activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding oxidoreductase activity NAD(P)H dehydrogenase (quinone) activity oxidoreductase activity, acting on NAD(P)H catalytic activity oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor NADH dehydrogenase (quinone) (non-electrogenic) activity NADH dehydrogenase activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding quinone binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding	aerobic respiration cellular respiration energy derivation by oxidation of organic compounds metabolic process cellular process generation of precursor metabolites and energy respiratory electron transport chain electron transport chain	cellular anatomical structure membrane respiratory chain complex protein-containing complex catalytic complex membrane protein complex transporter complex NADH dehydrogenase complex transmembrane transporter complex respiratory chain complex I oxidoreductase complex cell periphery plasma membrane
E [auth G]	NADH-quinone oxidoreductase subunit G	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding 2 iron, 2 sulfur cluster binding quinone binding molybdopterin cofactor binding cation binding ion binding metal ion binding	aerobic respiration cellular respiration energy derivation by oxidation of organic compounds metabolic process cellular process generation of precursor metabolites and energy oxidative phosphorylation respiratory electron transport chain ATP synthesis coupled electron transport electron transport chain	cellular anatomical structure membrane cell periphery plasma membrane intracellular anatomical structure cytoplasm protein-containing complex catalytic complex membrane protein complex oxidoreductase complex NADH dehydrogenase complex respiratory chain complex transporter complex transmembrane transporter complex cellular anatomical structure membrane cell periphery plasma membrane intracellular anatomical structure cytoplasm protein-containing complex catalytic complex membrane protein complex oxidoreductase complex NADH dehydrogenase complex respiratory chain complex transporter complex transmembrane transporter complex respiratory chain complex I
D [auth F]	NADH-quinone oxidoreductase subunit F	FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity quinone binding NAD binding purine nucleotide binding adenyl nucleotide binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding metal ion binding	aerobic respiration cellular respiration energy derivation by oxidation of organic compounds metabolic process cellular process generation of precursor metabolites and energy respiratory electron transport chain electron transport chain	cellular anatomical structure membrane respiratory chain complex protein-containing complex catalytic complex membrane protein complex transporter complex NADH dehydrogenase complex transmembrane transporter complex respiratory chain complex I oxidoreductase complex cell periphery plasma membrane
C [auth E]	NADH-quinone oxidoreductase subunit E	oxidoreductase activity catalytic activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding quinone binding cation binding ion binding metal ion binding	monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process generation of precursor metabolites and energy	cellular anatomical structure membrane respiratory chain complex protein-containing complex catalytic complex membrane protein complex transporter complex NADH dehydrogenase complex transmembrane transporter complex respiratory chain complex I oxidoreductase complex cell periphery plasma membrane
B [auth D]	NADH-quinone oxidoreductase subunit C/D	oxidoreductase activity NAD(P)H dehydrogenase (quinone) activity oxidoreductase activity, acting on NAD(P)H catalytic activity oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor NADH dehydrogenase (quinone) (non-electrogenic) activity NADH dehydrogenase activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity oxidoreductase activity NAD(P)H dehydrogenase (quinone) activity oxidoreductase activity, acting on NAD(P)H catalytic activity oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor NADH dehydrogenase (quinone) (non-electrogenic) activity NADH dehydrogenase activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity binding quinone binding small molecule binding NAD binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding	cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	cellular anatomical structure membrane respiratory chain complex protein-containing complex catalytic complex membrane protein complex transporter complex NADH dehydrogenase complex transmembrane transporter complex respiratory chain complex I oxidoreductase complex cell periphery plasma membrane intracellular anatomical structure cellular anatomical structure membrane respiratory chain complex protein-containing complex catalytic complex membrane protein complex transporter complex NADH dehydrogenase complex transmembrane transporter complex respiratory chain complex I oxidoreductase complex cell periphery plasma membrane intracellular anatomical structure cytoplasm
A [auth B]	NADH-quinone oxidoreductase subunit B	oxidoreductase activity NAD(P)H dehydrogenase (quinone) activity oxidoreductase activity, acting on NAD(P)H catalytic activity oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor NADH dehydrogenase (quinone) (non-electrogenic) activity NADH dehydrogenase activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding oxidoreductase activity NAD(P)H dehydrogenase (quinone) activity oxidoreductase activity, acting on NAD(P)H catalytic activity oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor NADH dehydrogenase (quinone) (non-electrogenic) activity NADH dehydrogenase activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity quinone binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding	electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport establishment of localization monoatomic cation transmembrane transport transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport aerobic respiration cellular respiration electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport establishment of localization monoatomic cation transmembrane transport transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport aerobic respiration cellular respiration energy derivation by oxidation of organic compounds metabolic process generation of precursor metabolites and energy respiratory electron transport chain electron transport chain	cellular anatomical structure membrane respiratory chain complex protein-containing complex catalytic complex membrane protein complex transporter complex NADH dehydrogenase complex transmembrane transporter complex respiratory chain complex I oxidoreductase complex cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth I]	IPR010226	NADH-quinone oxidoreductase, chain I	Family
F [auth I]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
F [auth I]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
E [auth G]	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
E [auth G]	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
E [auth G]	IPR054351	NADH-ubiquinone oxidoreductase, ferredoxin-like domain	Domain
E [auth G]	IPR010228	NADH:ubiquinone oxidoreductase, subunit G	Family
E [auth G]	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
E [auth G]	IPR050123	Prokaryotic molybdopterin-containing oxidoreductase	Family
E [auth G]	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
E [auth G]	IPR006656	Molybdopterin oxidoreductase	Domain
E [auth G]	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
E [auth G]	IPR000283	NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site	Conserved Site
E [auth G]	IPR019574	NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding	Domain
D [auth F]	IPR019575	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain	Domain
D [auth F]	IPR011537	NADH ubiquinone oxidoreductase, F subunit	Family
D [auth F]	IPR001949	NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site	Conserved Site
D [auth F]	IPR037225	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily	Homologous Superfamily
D [auth F]	IPR037207	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily	Homologous Superfamily
D [auth F]	IPR011538	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain	Domain
C [auth E]	IPR041921	NADH-quinone oxidoreductase subunit E, N-terminal	Homologous Superfamily
C [auth E]	IPR042128	NuoE domain	Domain
C [auth E]	IPR002023	NADH-quinone oxidoreductase subunit E-like	Family
C [auth E]	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
B [auth D]	IPR037232	NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily	Homologous Superfamily
B [auth D]	IPR023062	NADH dehydrogenase, subunit CD	Family
B [auth D]	IPR014029	NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site	Conserved Site
B [auth D]	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
B [auth D]	IPR022885	NAD(P)H-quinone oxidoreductase subunit D/H	Family
B [auth D]	IPR001268	NADH:ubiquinone oxidoreductase, 30kDa subunit	Domain
B [auth D]	IPR001135	NADH-quinone oxidoreductase, subunit D	Domain
B [auth D]	IPR020396	NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site	Conserved Site
B [auth D]	IPR010218	NADH dehydrogenase, subunit C	Family
A [auth B]	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
A [auth B]	IPR006138	NADH-ubiquinone oxidoreductase, 20 Kd subunit	Family

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth B], B [auth D], E [auth G], F [auth I]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex I	Complex I complete, focused refinement of cytoplasmic arm

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
D [auth F]	CSX	Parent Component: CYS RESID: AA0451 PSI-MOD : 2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380
C [auth E]	CSX	Parent Component: CYS RESID: AA0451 , AA0451 PSI-MOD : 2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380 , 2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380
A [auth B]	CSX	Parent Component: CYS RESID: AA0451 , AA0451 , AA0451 PSI-MOD : 2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380 , 2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380 , 2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380