Annotations: 6ZK9

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth 1]	d6zk913	All alpha proteins	Bromodomain-like	Nqo1C-terminal domain-like	automated matches	automated matches	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
A [auth 1]	d6zk911	Alpha and beta proteins (a/b)	Nqo1 FMN-binding domain-like	Nqo1 FMN-binding domain-like	automated matches	automated matches	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
A [auth 1]	d6zk912	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Nqo1 middle domain-like	automated matches	automated matches	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
N [auth g]	d6zk9g_	Membrane and cell surface proteins and peptides	LYR proteins from mammalian respiratory complex I	LYR protein-like	LYR proteins	automated matches	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
Q [auth j]	d6zk9j_	All alpha proteins	Acyl carrier protein-like	ACP-like	automated matches	automated matches	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
D [auth 4]	d6zk94_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J [auth c]	SCOP2B Superfamily	NADH-ubiquinone oxidoreductase-like	8053980	3002258	SCOP2B (2022-06-29)
B [auth 2]	SCOP2B Superfamily	Thioredoxin-like	8100908	3000031	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 [auth 1]	NADH_4Fe-4S	e6zk913	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)
A [auth 1]	SLBB	e6zk911	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Nqo1 middle domain-like	F: SLBB	ECOD (1.6)
A [auth 1]	Complex1_51K	e6zk912	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)
J [auth c]	ETC_C1_NDUFA4	e6zk9c1	A: a+b two layers	X: Putative oxidoreductase (From Topology)	H: Putative oxidoreductase (From Topology)	T: Putative oxidoreductase	F: ETC_C1_NDUFA4	ECOD (1.6)
K [auth d]	NAD_binding_10	e6zk9d1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_10	ECOD (1.6)
L [auth e]	L51_S25_CI-B8	e6zk9e1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: L51_S25_CI-B8	ECOD (1.6)
M [auth f]	ETC_C1_NDUFA5	e6zk9f1	A: extended segments	X: FATC domain (From Topology)	H: FATC domain (From Topology)	T: FATC domain	F: ETC_C1_NDUFA5	ECOD (1.6)
N [auth g]	Complex1_LYR	e6zk9g1	A: alpha bundles	X: LYR protein (From Topology)	H: LYR protein (From Topology)	T: LYR protein	F: Complex1_LYR	ECOD (1.6)
P [auth i]	NDUFA12	e6zk9i1	A: a+b three layers	X: Mitochondrial complex I, B17.2 subunit (From Topology)	H: Mitochondrial complex I, B17.2 subunit (From Topology)	T: Mitochondrial complex I, B17.2 subunit	F: NDUFA12	ECOD (1.6)
Q [auth j]	PP-binding	e6zk9j1	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP) (From Topology)	T: Acyl-carrier protein (ACP)	F: PP-binding	ECOD (1.6)
B [auth 2]	2Fe-2S_thioredx_N	e6zk922	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)
B [auth 2]	2Fe-2S_thioredx_C	e6zk921	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: 2Fe-2S_thioredx_C	ECOD (1.6)
C [auth 3]	PRK09129	e6zk932	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: PRK09129	ECOD (1.6)
C [auth 3]	Fer2_4	e6zk935	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_4	ECOD (1.6)
C [auth 3]	Molybdop_Fe4S4_1	e6zk934	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: Molybdop_Fe4S4_1	ECOD (1.6)
C [auth 3]	Molybdopterin_2nd	e6zk931	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: Molybdopterin_2nd	ECOD (1.6)
C [auth 3]	Molybdopterin_1st	e6zk936	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: Molybdopterin_1st	ECOD (1.6)
C [auth 3]	NADH-G_4Fe-4S_3	e6zk933	A: extended segments	X: iron-sulfur center-binding helical hairpin (From Topology)	H: iron-sulfur center-binding helical hairpin (From Topology)	T: iron-sulfur center-binding helical hairpin	F: NADH-G_4Fe-4S_3	ECOD (1.6)
D [auth 4]	Complex1_49kDa_1st	e6zk942	A: alpha complex topology	X: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	T: alpha-helical domain in nickel-iron hydrogenase, large subunit	F: Complex1_49kDa_1st	ECOD (1.6)
D [auth 4]	NuoD	e6zk943	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)	T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	F: NuoD	ECOD (1.6)
D [auth 4]	Complex1_49kDa_2nd	e6zk941	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)	T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	F: Complex1_49kDa_2nd	ECOD (1.6)
E [auth 5]	Complex1_30kDa	e6zk951	A: a+b two layers	X: Nqo5-like	H: Nqo5-like (From Topology)	T: Nqo5-like	F: Complex1_30kDa	ECOD (1.6)
F [auth 6]	Oxidored_q6	e6zk961	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
G [auth 9]	Fer4_21_1	e6zk991	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)
I [auth b]	zf-CHCC	e6zk9b1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Cytochrome c oxidase Subunit F	F: zf-CHCC	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth 1]	PF22461	SLBB domain (SLBB_2)	SLBB domain	This entry represents a set of SLBB domains [5].	Domain
A [auth 1]	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
A [auth 1]	PF10589	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region (NADH_4Fe-4S)	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region		Domain
B [auth 2]	PF01257	Thioredoxin-like [2Fe-2S] ferredoxin (2Fe-2S_thioredx)	Thioredoxin-like [2Fe-2S] ferredoxin	-	Family
E [auth 5]	PF00329	Respiratory-chain NADH dehydrogenase, 30 Kd subunit (Complex1_30kDa)	Respiratory-chain NADH dehydrogenase, 30 Kd subunit		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth 1]	NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial	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 oxidoreductase activity, acting on NAD(P)H 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 oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor NADH dehydrogenase activity oxidoreductase activity electron transfer activity active monoatomic ion transmembrane transporter activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity catalytic activity transmembrane transporter activity 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 aerobic electron transport chain oxidative phosphorylation energy derivation by oxidation of organic compounds ATP synthesis coupled electron transport electron transport chain generation of precursor metabolites and energy mitochondrial electron transport, NADH to ubiquinone respiratory electron transport chain metabolic process cellular process mitochondrial ATP synthesis coupled electron transport	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane
J [auth c]	NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial	-	electron transport chain metabolic process cellular process generation of precursor metabolites and energy	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane
K [auth d]	NADH:ubiquinone oxidoreductase subunit A9	-	-	-
L [auth e]	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2	-	-	-
M [auth f]	Mitochondrial complex I, B13 subunit	-	-	-
N [auth g]	NADH:ubiquinone oxidoreductase subunit A6	-	protein-containing complex organization NADH dehydrogenase complex assembly cellular component organization cellular component biogenesis organelle organization cellular component assembly mitochondrial respiratory chain complex assembly protein-containing complex assembly cellular process cellular component organization or biogenesis mitochondrial respiratory chain complex I assembly mitochondrion organization response to oxidative stress response to stimulus protein-containing complex organization NADH dehydrogenase complex assembly cellular component organization cellular component biogenesis organelle organization cellular component assembly mitochondrial respiratory chain complex assembly protein-containing complex assembly cellular process cellular component organization or biogenesis mitochondrial respiratory chain complex I assembly mitochondrion organization response to oxidative stress response to stimulus response to stress	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle 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
O [auth h]	Mitochondrial complex I, B14.5a subunit	-	aerobic respiration cellular respiration aerobic electron transport chain oxidative phosphorylation energy derivation by oxidation of organic compounds ATP synthesis coupled electron transport electron transport chain generation of precursor metabolites and energy mitochondrial electron transport, NADH to ubiquinone respiratory electron transport chain metabolic process cellular process mitochondrial ATP synthesis coupled electron transport	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane
P [auth i]	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12	-	-	-
Q [auth j]	Acyl carrier protein	phosphopantetheine-dependent carrier activity prosthetic group binding binding acyl carrier activity molecular carrier activity ACP phosphopantetheine attachment site binding acyl binding small molecule binding	-	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle
R [auth q]	Mitochondrial complex I, B16.6 subunit	-	-	-
B [auth 2]	Mitochondrial complex I, 24 kDa subunit	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on NAD(P)H catalytic activity NADH dehydrogenase activity cation binding ion binding metal ion binding	aerobic respiration cellular respiration aerobic electron transport chain oxidative phosphorylation energy derivation by oxidation of organic compounds ATP synthesis coupled electron transport electron transport chain generation of precursor metabolites and energy mitochondrial electron transport, NADH to ubiquinone respiratory electron transport chain metabolic process cellular process mitochondrial ATP synthesis coupled electron transport	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle
C [auth 3]	NADH:ubiquinone oxidoreductase core subunit S1	-	-	-
D [auth 4]	Mitochondrial complex I, 49 kDa subunit	-	-	-
E [auth 5]	NADH:ubiquinone oxidoreductase core subunit S3	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor NADH dehydrogenase activity oxidoreductase activity electron transfer activity active monoatomic ion transmembrane transporter activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor NADH dehydrogenase activity oxidoreductase activity electron transfer activity active monoatomic ion transmembrane transporter activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity catalytic activity transmembrane transporter activity	-	-
F [auth 6]	Mitochondrial complex I, PSST subunit	-	-	-
G [auth 9]	Mitochondrial complex I, TYKY subunit	-	-	-
H [auth a]	Mitochondrial complex I, 10 kDa subunit	-	-	-
I [auth b]	Mitochondrial complex I, 13 kDa subunit	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth 1]	IPR019575	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain	Domain
A [auth 1]	IPR054765	SLBB domain	Domain
A [auth 1]	IPR011537	NADH ubiquinone oxidoreductase, F subunit	Family
A [auth 1]	IPR001949	NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site	Conserved Site
A [auth 1]	IPR037225	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily	Homologous Superfamily
A [auth 1]	IPR037207	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily	Homologous Superfamily
A [auth 1]	IPR011538	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain	Domain
A [auth 1]	IPR050837	Complex I 51 kDa subunit	Family
J [auth c]	IPR038532	NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily	Homologous Superfamily
J [auth c]	IPR006885	NADH dehydrogenase ubiquinone Fe-S protein 4 mitochondrial-like	Family
N [auth g]	IPR016488	NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6	Family
N [auth g]	IPR008011	Complex 1 LYR protein domain	Domain
N [auth g]	IPR045299	NDUFA6, LYR domain	Domain
O [auth h]	IPR009947	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7	Family
Q [auth j]	IPR006162	Phosphopantetheine attachment site	PTM
Q [auth j]	IPR009081	Phosphopantetheine binding ACP domain	Domain
Q [auth j]	IPR036736	ACP-like superfamily	Homologous Superfamily
Q [auth j]	IPR003231	Acyl carrier protein	Family
B [auth 2]	IPR042128	NuoE domain	Domain
B [auth 2]	IPR002023	NADH-quinone oxidoreductase subunit E-like	Family
B [auth 2]	IPR041921	NADH-quinone oxidoreductase subunit E, N-terminal	Homologous Superfamily
B [auth 2]	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
E [auth 5]	IPR037232	NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily	Homologous Superfamily
E [auth 5]	IPR001268	NADH:ubiquinone oxidoreductase, 30kDa subunit	Domain
E [auth 5]	IPR020396	NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site	Conserved Site
E [auth 5]	IPR010218	NADH dehydrogenase, subunit C	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth 1], J [auth c], N [auth g], O [auth h]	OPM	Transmembrane	Alpha-helical polytopic	Electron transport chain complex I (NADH dehydrogenase) and supercomplexes	H+ or Na+ translocating NADH dehydrogenase

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth 1], J [auth c], N [auth g], O [auth h]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex I	Mitochondrial Complex I: native complex, closed

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
O [auth h]	AYA	Parent Component: ALA
D [auth 4]	2MR	Parent Component: ARG RESID: AA0067 PSI-MOD : symmetric dimethyl-L-arginine MOD:00076