5EAI | pdb_00005eai

Crystal Structure of NAD(P)H dehydrogenase, quinone 1 complexed with a chemotherapeutic naphthoquinone E6a

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
N	d5eain_	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	Quinone reductase	NAD(P)H:quinone reductase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
M	d5eaim_	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	Quinone reductase	NAD(P)H:quinone reductase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
L	d5eail_	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	Quinone reductase	NAD(P)H:quinone reductase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K	d5eaik_	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	Quinone reductase	NAD(P)H:quinone reductase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d5eaij_	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	Quinone reductase	NAD(P)H:quinone reductase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d5eaii_	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	Quinone reductase	NAD(P)H:quinone reductase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d5eaih_	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	Quinone reductase	NAD(P)H:quinone reductase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d5eaig_	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	Quinone reductase	NAD(P)H:quinone reductase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d5eaif_	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	Quinone reductase	NAD(P)H:quinone reductase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d5eaie_	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	d5eaid_	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	d5eaic_	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	Quinone reductase	NAD(P)H:quinone reductase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5eaib_	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	d5eaia_	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)
N	SCOP2B Superfamily	Flavoproteins	8044090	3001217	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Flavoproteins	8044090	3001217	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Flavoproteins	8044090	3001217	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Flavoproteins	8044090	3001217	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Flavoproteins	8044090	3001217	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Flavoproteins	8044090	3001217	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Flavoproteins	8044090	3001217	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Flavoproteins	8044090	3001217	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Flavoproteins	8044090	3001217	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Flavoproteins	8044090	3001217	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Flavoproteins	8044090	3001217	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Flavoproteins	8044090	3001217	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Flavoproteins	8044090	3001217	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Flavoproteins	8044090	3001217	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)
N	Glyco_hydro_31_2nd	e5eaiN1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (develop294)
M	Glyco_hydro_31_2nd	e5eaiM1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (develop294)
L	Glyco_hydro_31_2nd	e5eaiL1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (develop294)
K	Glyco_hydro_31_2nd	e5eaiK1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (develop294)
J	Glyco_hydro_31_2nd	e5eaiJ1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (develop294)
I	Glyco_hydro_31_2nd	e5eaiI1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (develop294)
H	Glyco_hydro_31_2nd	e5eaiH1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (develop294)
G	Glyco_hydro_31_2nd	e5eaiG1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (develop294)
F	Glyco_hydro_31_2nd	e5eaiF1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (develop294)
E	Glyco_hydro_31_2nd	e5eaiE1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (develop294)
D	Glyco_hydro_31_2nd	e5eaiD1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (develop294)
C	Glyco_hydro_31_2nd	e5eaiC1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (develop294)
B	Glyco_hydro_31_2nd	e5eaiB1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (develop294)
A	Glyco_hydro_31_2nd	e5eaiA1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
N	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
M	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
L	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
K	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
J	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
I	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
H	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
G	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
F	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
E	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)
C	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
B	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, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	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, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	NAD(P)H dehydrogenase [quinone] 1	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 cytochrome-b5 reductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor NADPH dehydrogenase activity NADPH dehydrogenase (quinone) activity RNA binding binding nucleic acid 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 cytochrome-b5 reductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor NADPH dehydrogenase activity NADPH dehydrogenase (quinone) activity RNA binding binding nucleic acid binding identical protein binding protein binding	vitamin E metabolic process metabolic process cellular process cellular response to stimulus response to stimulus cellular response to oxidative stress detoxification reactive oxygen species metabolic process cellular response to chemical stress response to superoxide cellular oxidant detoxification cellular response to oxygen radical cellular response to reactive oxygen species cellular response to stress vitamin E metabolic process metabolic process cellular process cellular response to stimulus response to stimulus cellular response to oxidative stress detoxification reactive oxygen species metabolic process cellular response to chemical stress response to superoxide cellular oxidant detoxification cellular response to oxygen radical cellular response to reactive oxygen species cellular response to stress response to stress cellular detoxification response to oxygen-containing compound cellular response to oxygen-containing compound response to reactive oxygen species response to toxic substance removal of superoxide radicals superoxide metabolic process response to oxidative stress cellular response to chemical stimulus response to chemical cellular response to superoxide cellular response to toxic substance response to oxygen radical ketone metabolic process ubiquinone metabolic process quinone metabolic process 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 primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process negative regulation of ferroptosis regulation of biological process regulation of cellular process negative regulation of programmed cell death biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of cellular process regulation of ferroptosis ferroptosis programmed cell death response to nutrient levels response to caloric restriction 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 cellular response to xenobiotic stimulus xenobiotic metabolic process response to xenobiotic stimulus cell redox homeostasis cellular homeostasis homeostatic process negative regulation of protein catabolic process regulation of primary metabolic 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 trans-synaptic signaling signaling cell-cell signaling chemical synaptic transmission cell communication synaptic signaling anterograde trans-synaptic signaling synaptic transmission, cholinergic response to lipid response to lipopolysaccharide response to bacterium response to molecule of bacterial origin vitamin K metabolic process nitric oxide metabolic process nitric oxide biosynthetic process biosynthetic process reactive nitrogen species metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol 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, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR003680	Flavodoxin-like fold	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR029039	Flavoprotein-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR051545	NAD(P)H dehydrogenase (quinone)	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	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 kidney disease Parkinson 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 lung cancer benign neoplasm subependymal giant cell astrocytoma myopathy colorectal carcinoma endometriosis ovarian cancer pancreatic intraductal papillary-mucinous neoplasm invasive ductal breast carcinoma papillomatosis large cell medulloblastoma attention deficit hyperactivity disorder, inattentive type psoriasis childhood acute lymphoblastic leukemia chronic obstructive pulmonary disease nasopharyngeal carcinoma urinary bladder neoplasm cutaneous lupus erythematosus diastrophic dysplasia head and neck cancer pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia plasma cell neoplasm lung adenocarcinoma atypical teratoid rhabdoid tumor malignant pancreatic neoplasm schizophrenia medulloblastoma myeloid neoplasm toxic encephalopathy

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.