3QFC | pdb_00003qfc

Crystal Structure of Human NADPH-Cytochrome P450 (V492E mutant)

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)
A	d3qfca2	All beta proteins	Reductase/isomerase/elongation factor common domain	Riboflavin synthase domain-like	NADPH-cytochrome p450 reductase FAD-binding domain-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3qfca1	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3qfca3	Alpha and beta proteins (a/b)	Ferredoxin reductase-like, C-terminal NADP-linked domain	Ferredoxin reductase-like, C-terminal NADP-linked domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3qfcb2	All beta proteins	Reductase/isomerase/elongation factor common domain	Riboflavin synthase domain-like	NADPH-cytochrome p450 reductase FAD-binding domain-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3qfcb1	Alpha and beta proteins (a/b)	Flavodoxin-like	Flavoproteins	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3qfcb3	Alpha and beta proteins (a/b)	Ferredoxin reductase-like, C-terminal NADP-linked domain	Ferredoxin reductase-like, C-terminal NADP-linked domain	automated matches	automated matches	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)
A	SCOP2B Superfamily	Flavoproteins	8044084	3001217	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Flavoproteins	8044084	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)
A		e3qfcA1	A: Thioredoxin-like	X: Thioredoxin-like	H: Thioredoxin-like	T: THUMP	F:	ECOD (20:10:01)
B		e3qfcB3	A: DP domain	X: DP domain	H: DP domain	T: YonK	F:	ECOD (20:10:01)
B		e3qfcB5	A: Thioredoxin-like	X: Thioredoxin-like	H: Thioredoxin-like	T: THUMP	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
A	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
A	1.20.990.10	Mainly Alpha	Up-down Bundle	NADPH-cytochrome p450 Reductase	Chain A, domain 3	CATH (4.3.0)
A	3.40.50.80	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module	CATH (4.3.0)
B	3.40.50.360	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Flavodoxin domain	CATH (4.3.0)
B	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B	1.20.990.10	Mainly Alpha	Up-down Bundle	NADPH-cytochrome p450 Reductase	Chain A, domain 3	CATH (4.3.0)
B	3.40.50.80	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00667	FAD binding domain (FAD_binding_1)	FAD binding domain	This domain is found in sulfite reductase, NADPH cytochrome P450 reductase, Nitric oxide synthase and methionine synthase reductase. This domain consists of a RIFT-like beta-barrel containing an inserted alpha-helical subdomain.	Domain
A, B	PF00175	Oxidoreductase NAD-binding domain (NAD_binding_1)	Oxidoreductase NAD-binding domain	Xanthine dehydrogenases, that also bind FAD/NAD, have essentially no similarity.	Domain
A, B	PF00258	Flavodoxin (Flavodoxin_1)	Flavodoxin		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	NADPH--cytochrome P450 reductase	FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding flavin adenine dinucleotide binding oxidoreductase activity cytochrome-b5 reductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding flavin adenine dinucleotide binding oxidoreductase activity cytochrome-b5 reductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor catalytic activity hydrolase activity electron transfer activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen nitric oxide dioxygenase NAD(P)H activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donor dioxygenase activity purine nucleotide binding adenyl nucleotide binding NADP binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity NADPH-hemoprotein reductase activity iron-cytochrome-c reductase activity oxidoreductase activity, acting on a heme group of donors protein binding enzyme binding	response to stimulus response to chemical response to xenobiotic stimulus nitric oxide metabolic process catabolic process nitric oxide catabolic process metabolic process cellular process reactive nitrogen species metabolic process cellular response to stimulus cellular response to nitrogen compound response to endogenous stimulus response to peptide hormone cellular response to peptide hormone stimulus response to stimulus response to chemical response to xenobiotic stimulus nitric oxide metabolic process catabolic process nitric oxide catabolic process metabolic process cellular process reactive nitrogen species metabolic process cellular response to stimulus cellular response to nitrogen compound response to endogenous stimulus response to peptide hormone cellular response to peptide hormone stimulus response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone cellular response to hormone stimulus regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death organohalogen metabolic process organofluorine metabolic process positive regulation of cell communication positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of smoothened signaling pathway signal transduction positive regulation of cellular process regulation of smoothened signaling pathway regulation of signaling cell surface receptor signaling pathway smoothened signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling multicellular organismal process regulation of cartilage development regulation of chondrocyte differentiation regulation of developmental process connective tissue development cellular developmental process regulation of cell differentiation positive regulation of chondrocyte differentiation positive regulation of developmental process multicellular organism development skeletal system development positive regulation of cell differentiation cell differentiation anatomical structure development regulation of multicellular organismal process system development developmental process regulation of multicellular organismal development animal organ development tissue development chondrocyte differentiation positive regulation of multicellular organismal process positive regulation of cartilage development cartilage development demethylation regulation of steroid biosynthetic process positive regulation of steroid hormone biosynthetic process regulation of hormone biosynthetic process regulation of hormone metabolic process regulation of lipid metabolic process steroid metabolic process lipid biosynthetic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of lipid metabolic process regulation of biological quality hormone biosynthetic process steroid biosynthetic process regulation of biosynthetic process regulation of steroid hormone biosynthetic process positive regulation of hormone metabolic process regulation of hormone levels regulation of steroid metabolic process primary metabolic process hormone metabolic process positive regulation of steroid biosynthetic process biosynthetic process positive regulation of lipid biosynthetic process positive regulation of steroid metabolic process positive regulation of hormone biosynthetic process regulation of lipid biosynthetic process regulation of metabolic process lipid metabolic process electron transport chain generation of precursor metabolites and energy response to ketone response to lipid response to glucocorticoid response to corticosteroid response to steroid hormone response to dexamethasone oxoacid metabolic process nitrate catabolic process small molecule metabolic process organic acid metabolic process nitrate metabolic process flavonoid metabolic process cellular response to gonadotropin stimulus response to gonadotropin cellular response to follicle-stimulating hormone stimulus response to follicle-stimulating hormone fatty acid metabolic process carboxylic acid metabolic process lipid modification fatty acid oxidation lipid oxidation monocarboxylic acid metabolic process P450-containing electron transport chain positive regulation of cell population proliferation developmental growth endochondral bone morphogenesis organ growth growth plate cartilage chondrocyte proliferation regulation of growth plate cartilage chondrocyte proliferation growth plate cartilage development endochondral bone growth animal organ morphogenesis bone development cell population proliferation growth anatomical structure morphogenesis positive regulation of growth plate cartilage chondrocyte proliferation regulation of cell population proliferation bone growth skeletal system morphogenesis cartilage development involved in endochondral bone morphogenesis bone morphogenesis carnitine metabolic process modified amino acid metabolic process amino-acid betaine metabolic process response to nutrient levels response to nutrient nitric oxide biosynthetic process	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001709	Flavoprotein pyridine nucleotide cytochrome reductase	Domain
A, B	IPR001433	Oxidoreductase FAD/NAD(P)-binding	Domain
A, B	IPR003097	Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding	Domain
A, B	IPR017938	Riboflavin synthase-like beta-barrel	Homologous Superfamily
A, B	IPR001094	Flavodoxin-like	Domain
A, B	IPR023173	NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily	Homologous Superfamily
A, B	IPR008254	Flavodoxin/nitric oxide synthase	Domain
A, B	IPR023208	NADPH-cytochrome P450 reductase	Family
A, B	IPR039261	Ferredoxin-NADP reductase (FNR), nucleotide-binding domain	Homologous Superfamily
A, B	IPR017927	FAD-binding domain, ferredoxin reductase-type	Domain
A, B	IPR029039	Flavoprotein-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P16435	craniosynostosis congenital adrenal hyperplasia gliosarcoma urinary bladder cancer amenorrhea Antley-Bixler syndrome Antley-Bixler syndrome with genital anomalies and disordered steroidogenesis Learning Disturbance ovarian cancer learning disability malignant mesothelioma pancreatic ductal adenocarcinoma psoriasis urinary bladder neoplasm arthrogryposis craniosynostosis congenital adrenal hyperplasia gliosarcoma urinary bladder cancer amenorrhea Antley-Bixler syndrome Antley-Bixler syndrome with genital anomalies and disordered steroidogenesis Learning Disturbance ovarian cancer learning disability malignant mesothelioma pancreatic ductal adenocarcinoma psoriasis urinary bladder neoplasm arthrogryposis pituitary cancer tuberculosis astrocytic tumor congenital adrenal hyperplasia due to cytochrome P450 oxidoreductase deficiency

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.