5YJX | pdb_00005yjx

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with myxothiazol.

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	OB_NTP_bind	e5yjxB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: OB_NTP_bind	ECOD (v294.1)
A	14-3-3	e5yjxA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: 14-3-3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.50.50.100	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain		CATH (utative)
A	3.50.50.100	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF22366	NDH2 C-terminal domain (NDH2_C)	NDH2 C-terminal domain	This entry represent the C-terminal domain of alternative NADH:quinone oxidoreductases known as NDH2 that deliver electrons to the respiratory chain by oxidation of NADH and reduction of quinones but does not pump protons. NDH-2 have particular relev ...	This entry represent the C-terminal domain of alternative NADH:quinone oxidoreductases known as NDH2 that deliver electrons to the respiratory chain by oxidation of NADH and reduction of quinones but does not pump protons. NDH-2 have particular relevance in yeasts like Saccharomyces cerevisiae and in several prokaryotes, whose respiratory chains are devoid of complex I, in which NDH-2 keep the balance and are the main entry point of electrons into the respiratory chains [2]. NDH2 proteins are found in bacteria, certain plant, fungal and protozoan mitochondria, but not in mammals, they have been used as a drug target for Mycoplasma tuberculosis, Plasmodium falciparum and Toxoplasma gondii [1,3].	Domain
A, B	PF07992	Pyridine nucleotide-disulphide oxidoreductase (Pyr_redox_2)	Pyridine nucleotide-disulphide oxidoreductase	This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial	oxidoreductase activity catalytic activity NAD(P)H dehydrogenase (quinone) activity NADH dehydrogenase (ubiquinone) (non-electrogenic) activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor NADH dehydrogenase (quinone) (non-electrogenic) activity NADH dehydrogenase activity identical protein binding protein binding binding	regulation of biological process positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process cellular process apoptotic process programmed cell death positive regulation of cellular process aerobic respiration regulation of biological process positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process cellular process apoptotic process programmed cell death positive regulation of cellular process 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 mitochondrial ATP synthesis coupled electron transport	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR054585	External alternative NADH-ubiquinone oxidoreductase-like, C-terminal domain	Domain
A, B	IPR023753	FAD/NAD(P)-binding domain	Domain
A, B	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR045024	Alternative NADH dehydrogenase	Family

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.