6BDO | pdb_00006bdo

Structure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with a quinone inhibitor HQNO at 2.8A resolution

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)
D [auth C]	VP4_haemagglut	e6bdoC1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: VP4_haemagglut	ECOD (v294.1)
C [auth D]	V-set	e6bdoD1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Ribosomal protein S5 domain 2-like	T: Ribosomal protein S5 domain 2-like	F: V-set	ECOD (v294.1)
B [auth A]	VP4_haemagglut	e6bdoA1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: VP4_haemagglut	ECOD (v294.1)
A [auth B]	VP4_haemagglut	e6bdoB1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: VP4_haemagglut	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth C]	3.50.50.100	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain		CATH (4.3.0)
C [auth D]	3.50.50.100	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain		CATH (4.3.0)
B [auth A]	3.50.50.100	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain		CATH (4.3.0)
A [auth B]	3.50.50.100	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth A], C [auth D], D [auth C]	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 [auth B], B [auth A], C [auth D], D [auth C]	FAD-dependent pyridine nucleotide-disulfide oxidoreductase	oxidoreductase activity NAD(P)H dehydrogenase (quinone) activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor catalytic activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding	aerobic electron transport chain aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A], C [auth D], D [auth C]	IPR023753	FAD/NAD(P)-binding domain	Domain
A [auth B], B [auth A], C [auth D], D [auth C]	IPR051169	NADH:quinone oxidoreductase/NAD(P)H-quinone oxidoreductase	Family
A [auth B], B [auth A], C [auth D], D [auth C]	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily

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.