1D4A

CRYSTAL STRUCTURE OF HUMAN NAD[P]H-QUINONE OXIDOREDUCTASE AT 1.7 A RESOLUTION

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1d4ab_	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	Quinone reductase	NAD(P)H:quinone reductase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1d4ac_	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	Quinone reductase	NAD(P)H:quinone reductase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1d4ad_	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	Quinone reductase	NAD(P)H:quinone reductase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1d4aa_	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	Quinone reductase	NAD(P)H:quinone reductase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Flavoproteins	8044090	3001217	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Flavoproteins	8044090	3001217	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Flavoproteins	8044090	3001217	SCOP2B (2022-06-29)
A	SCOP2 Family	Quinone reductase	8031712	4003674	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Flavoproteins	8044090	3001217	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)
B	FMN_red	e1d4aB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: Flavoproteins	F: FMN_red	ECOD (1.6)
C	FMN_red	e1d4aC1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: Flavoproteins	F: FMN_red	ECOD (1.6)
D	FMN_red	e1d4aD1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: Flavoproteins	F: FMN_red	ECOD (1.6)
A	FMN_red	e1d4aA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: Flavoproteins	F: FMN_red	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
C	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
D	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
A	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02525	Flavodoxin-like fold (Flavodoxin_2)	Flavodoxin-like fold	This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) EC:1.6.99.2. These enzymes catalyse the NAD(P)H-dependent two-electron reductions of quinones and protect cell ...	This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) EC:1.6.99.2. These enzymes catalyse the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species [1]. This enzyme uses a FAD co-factor. The equation for this reaction is:- NAD(P)H + acceptor <=> NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy [1]. The family also includes acyl carrier protein phosphodiesterase EC:3.1.4.14. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP [2]. This family is related to Pfam:PF03358 and Pfam:PF00258.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	QUINONE REDUCTASE	oxidoreductase activity NADH:ubiquinone reductase (non-electrogenic) 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 activity cytochrome-b5 reductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor NAD(P)H dehydrogenase (quinone) activity identical protein binding protein binding binding superoxide dismutase activity oxidoreductase activity, acting on superoxide radicals as acceptor oxidoreductase activity NADH:ubiquinone reductase (non-electrogenic) 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 activity cytochrome-b5 reductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor NAD(P)H dehydrogenase (quinone) activity identical protein binding protein binding binding superoxide dismutase activity oxidoreductase activity, acting on superoxide radicals as acceptor antioxidant activity NADPH dehydrogenase (quinone) activity RNA binding organic cyclic compound binding nucleic acid binding	response to stimulus response to stress response to ischemia response to ketone response to lipid response to chemical response to oxygen-containing compound response to testosterone response to organic cyclic compound biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to stimulus response to stress response to ischemia response to ketone response to lipid response to chemical response to oxygen-containing compound response to testosterone response to organic cyclic compound biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism innate immune response response to external biotic stimulus catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process regulation of biological process neuron apoptotic 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 apoptotic process positive regulation of neuron apoptotic process programmed cell death positive regulation of cellular process regulation of neuron apoptotic process cellular response to stimulus cellular response to metal ion cellular response to chemical stimulus response to metal ion response to toxic substance response to oxidative stress cellular response to stress cellular response to oxidative stress cellular response to chemical stress response to electrical stimulus response to abiotic stimulus protein polyubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal cell redox homeostasis cellular homeostasis homeostatic process negative regulation of biological process negative regulation of protein catabolic process regulation of primary metabolic process negative regulation of cellular process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process regulation of protein metabolic process negative regulation of metabolic process regulation of macromolecule metabolic process regulation of catabolic process regulation of metabolic process regulation of protein catabolic process response to hydrogen sulfide response to hormone response to endogenous stimulus response to acid chemical response to L-glutamine response to nitrogen compound response to amino acid nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process nucleotide metabolic process NADH oxidation NAD metabolic process NADH metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process pyridine nucleotide metabolic process vitamin E metabolic process fat-soluble vitamin metabolic process organic hydroxy compound metabolic process vitamin metabolic process detoxification reactive oxygen species metabolic process response to superoxide cellular oxidant detoxification cellular response to oxygen radical cellular response to reactive oxygen species cellular detoxification cellular response to oxygen-containing compound response to reactive oxygen species removal of superoxide radicals superoxide metabolic process cellular response to superoxide cellular response to toxic substance response to oxygen radical negative regulation of programmed cell death negative regulation of apoptotic process ketone metabolic process ubiquinone metabolic process quinone metabolic process NADP metabolic process NADPH oxidation negative regulation of ferroptosis regulation of ferroptosis ferroptosis response to alcohol response to ethanol cellular response to hydrogen peroxide response to hydrogen peroxide response to flavonoid cellular response to xenobiotic stimulus xenobiotic metabolic process response to xenobiotic stimulus response to alkaloid response to nutrient levels response to nutrient trans-synaptic signaling signaling cell-cell signaling chemical synaptic transmission cell communication synaptic signaling anterograde trans-synaptic signaling synaptic transmission, cholinergic response to lipopolysaccharide response to bacterium response to molecule of bacterial origin vitamin K metabolic process response to amine response to carbohydrate response to estradiol response to tetrachloromethane nitric oxide metabolic process nitric oxide biosynthetic process biosynthetic process reactive nitrogen species metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection cell body neuronal cell body synapse cell junction cellular anatomical structure intracellular anatomical structure cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection cell body neuronal cell body synapse cell junction membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR003680	Flavodoxin-like fold	Domain
A, B, C, D	IPR029039	Flavoprotein-like superfamily	Homologous Superfamily
A, B, C, D	IPR051545	NAD(P)H dehydrogenase (quinone)	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P15559	non-small cell lung carcinoma hemolytic-uremic syndrome spinocerebellar ataxia type 17 cancer plasma cell myeloma myeloid leukemia contact dermatitis papilloma liver disease chronic monocytic leukemia urinary bladder cancer Neoplasms, Experimental obesity disorder breast cancer squamous papilloma non-small cell lung carcinoma hemolytic-uremic syndrome spinocerebellar ataxia type 17 cancer plasma cell myeloma myeloid leukemia contact dermatitis papilloma liver disease chronic monocytic leukemia urinary bladder cancer Neoplasms, Experimental obesity disorder breast cancer squamous papilloma hyperglycemia Parkinson disease kidney disease asthma prostate cancer breast carcinoma cholestasis colorectal cancer diabetes mellitus osteoarthritis pancreatic intraductal papillary-mucinous carcinoma acute kidney failure plantar fibromatosis alcohol withdrawal astrocytic tumor benign neoplasm lung cancer subependymal giant cell astrocytoma colorectal carcinoma myopathy ovarian cancer endometriosis pancreatic intraductal papillary-mucinous neoplasm papillomatosis invasive ductal breast carcinoma large cell medulloblastoma attention deficit hyperactivity disorder, inattentive type psoriasis childhood acute lymphoblastic leukemia chronic obstructive pulmonary disease urinary bladder neoplasm nasopharyngeal carcinoma cutaneous lupus erythematosus diastrophic dysplasia pancreatic ductal adenocarcinoma head and neck cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia plasma cell neoplasm atypical teratoid rhabdoid tumor lung adenocarcinoma schizophrenia malignant pancreatic neoplasm medulloblastoma toxic encephalopathy myeloid neoplasm

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	NAD(P)H dehydrogenase (quinone) M-CSA #3	Quinone reductase exists as a dimer of identical subunits, each comprising of 273 amino acids with two identical catalytic sites at equivalent positions. The enzyme catalyses the FAD dependent reduction of quinones. The dimer binds two FAD cofactors which remain non-covalently bound during catalysis. NAD(P)H and NAD(P)+ cycle in and out of the catalytic site. The catalytic domain has the characteristic twisted central parallel beta sheet surrounded on both sides by connecting helices, as found in other flavoproteins.	Defined by 3 residues: GLY:A-149TYR:A-155HIS:A-161 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.6.99.2 (PDB Primary Data) Search M-CSA Motif + EC 1.6.99.2 EC: 1.6.5.2 (UniProt) Search M-CSA Motif + EC 1.6.5.2

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.