7Q5Y | pdb_00007q5y

Structure of NADH:ubichinon oxidoreductase (complex I) of the hyperthermophilic eubacterium Aquifex aeolicus

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
K	SCOP2B Superfamily	Thioredoxin-like	8098206	3000031	SCOP2B (2022-06-29)
W	SCOP2B Superfamily	Thioredoxin-like	8098206	3000031	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Thioredoxin-like	8098206	3000031	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Thioredoxin-like	8098206	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)
X	tRNA-synt_2	e7q5yX1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.1)
R	tRNA-synt_2	e7q5yR1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.1)
L	tRNA-synt_2	e7q5yL1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.1)
F	tRNA-synt_2	e7q5yF1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.1)
K	tRNA-synt_2	e7q5yK1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.1)
W	tRNA-synt_2	e7q5yW1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.1)
Q	tRNA-synt_2	e7q5yQ1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.1)
E	tRNA-synt_2	e7q5yE1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.1)
D		e7q5yD01	A: a/b three-layered sandwiches	X: Rossmann-like	H: all-alpha NTP pyrophosphatases	T: Hypothetical protein AF_0060	F:	ECOD (v294.1)
U	tRNA-synt_2	e7q5yU1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.1)
O	tRNA-synt_2	e7q5yO1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.1)
I	tRNA-synt_2	e7q5yI1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.1)
C	tRNA-synt_2	e7q5yC1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.1)
B		e7q5yB01	A: a/b three-layered sandwiches	X: Rossmann-like	H: all-alpha NTP pyrophosphatases	T: Hypothetical protein AF_0060	F:	ECOD (v294.1)
A		e7q5yA01	A: a/b three-layered sandwiches	X: Rossmann-like	H: all-alpha NTP pyrophosphatases	T: Hypothetical protein AF_0060	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
V	3.30.70.3270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (utative)
P	3.30.70.3270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (utative)
J	3.30.70.3270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (utative)
D	3.30.70.3270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (utative)
U	3.10.20.600	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (utative)
U	1.20.1440.230	Mainly Alpha	Up-down Bundle	de novo design (two linked rop proteins)	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain	CATH (utative)
O	3.10.20.600	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (utative)
O	1.20.1440.230	Mainly Alpha	Up-down Bundle	de novo design (two linked rop proteins)	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain	CATH (utative)
I	3.10.20.600	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (utative)
I	1.20.1440.230	Mainly Alpha	Up-down Bundle	de novo design (two linked rop proteins)	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain	CATH (utative)
C	3.10.20.600	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (utative)
C	1.20.1440.230	Mainly Alpha	Up-down Bundle	de novo design (two linked rop proteins)	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain	CATH (utative)
T	3.30.460.80	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (utative)
T	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (utative)
N	3.30.460.80	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (utative)
N	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (utative)
H	3.30.460.80	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (utative)
H	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (utative)
B	3.30.460.80	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (utative)
B	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (utative)
G	3.10.20.740	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (utative)
M	3.10.20.740	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
F, L, R, X	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit		Domain
E, K, Q, W	PF01257	Thioredoxin-like [2Fe-2S] ferredoxin (2Fe-2S_thioredx)	Thioredoxin-like [2Fe-2S] ferredoxin	-	Family
D, J, P, V	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
D, J, P, V	PF12800	4Fe-4S binding domain (Fer4_4)	4Fe-4S binding domain	This 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, I, O, U	PF10531	SLBB domain (SLBB)	SLBB domain		Domain
C, I, O, U	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
C, I, O, U	PF10589	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region (NADH_4Fe-4S)	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region		Domain
B, H, N, T	PF00329	Respiratory-chain NADH dehydrogenase, 30 Kd subunit (Complex1_30kDa)	Respiratory-chain NADH dehydrogenase, 30 Kd subunit		Domain
B, H, N, T	PF00346	Respiratory-chain NADH dehydrogenase, 49 Kd subunit (Complex1_49kDa)	Respiratory-chain NADH dehydrogenase, 49 Kd subunit	-	Family
A, G, M, S	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, G, M, S	PF00111	2Fe-2S iron-sulfur cluster binding domain (Fer2)	2Fe-2S iron-sulfur cluster binding domain		Domain
A, G, M, S	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
A, G, M, S	PF10588	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region (NADH-G_4Fe-4S_3)	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F, L, R, X	NADH-quinone oxidoreductase subunit B	iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding transition metal ion binding iron ion binding ion binding metal ion 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 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 quinone 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 chain complex protein-containing complex catalytic complex membrane membrane protein complex transporter complex NADH dehydrogenase complex cellular anatomical structure transmembrane transporter complex respiratory chain complex I oxidoreductase complex cell periphery plasma membrane
E, K, Q, W	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 cation binding ion binding metal ion binding quinone 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	-
D, J, P, V	NADH-quinone oxidoreductase subunit I	iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding oxidoreductase activity NAD(P)H dehydrogenase (quinone) activity oxidoreductase activity, acting on NAD(P)H catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding transition metal ion binding iron ion binding ion binding metal ion 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 quinone binding	-	cell periphery cellular anatomical structure plasma membrane membrane
C, I, O, U	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 iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding metal ion 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	-	-
B, H, N, T	NADH-quinone oxidoreductase subunit C/D 2	NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound 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 NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound 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 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 quinone binding	-	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex catalytic complex membrane protein complex oxidoreductase complex NADH dehydrogenase complex
A, G, M, S	NADH dehydrogenase I chain G	oxidoreductase activity catalytic activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster 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 oxidoreductase activity catalytic activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster 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 4 iron, 4 sulfur cluster binding cation binding ion binding metal ion binding	aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds respiratory electron transport chain ATP synthesis coupled electron transport electron transport chain 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
F, L, R, X	IPR006138	NADH-ubiquinone oxidoreductase, 20 Kd subunit	Family
F, L, R, X	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
E, K, Q, W	IPR042128	NuoE domain	Domain
E, K, Q, W	IPR002023	NADH-quinone oxidoreductase subunit E-like	Family
E, K, Q, W	IPR041921	NADH-quinone oxidoreductase subunit E, N-terminal	Homologous Superfamily
E, K, Q, W	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
D, J, P, V	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
D, J, P, V	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
D, J, P, V	IPR010226	NADH-quinone oxidoreductase, chain I	Family
C, I, O, U	IPR019575	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain	Domain
C, I, O, U	IPR001949	NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site	Conserved Site
C, I, O, U	IPR019554	Soluble ligand binding domain	Domain
C, I, O, U	IPR037225	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily	Homologous Superfamily
C, I, O, U	IPR037207	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily	Homologous Superfamily
C, I, O, U	IPR011538	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain	Domain
B, H, N, T	IPR037232	NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily	Homologous Superfamily
B, H, N, T	IPR022885	NAD(P)H-quinone oxidoreductase subunit D/H	Family
B, H, N, T	IPR001268	NADH:ubiquinone oxidoreductase, 30kDa subunit	Domain
B, H, N, T	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
B, H, N, T	IPR001135	NADH-quinone oxidoreductase, subunit D	Domain
B, H, N, T	IPR026662	NADH-quinone oxidoreductase subunit CD	Family
A, G, M, S	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
A, G, M, S	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
A, G, M, S	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
A, G, M, S	IPR000283	NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site	Conserved Site
A, G, M, S	IPR054351	NADH-ubiquinone oxidoreductase, ferredoxin-like domain	Domain
A, G, M, S	IPR050123	Prok_molybdopt-oxidoreductase	Unknown
A, G, M, S	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A, G, M, S	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A, G, M, S	IPR019574	NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding	Domain