3WKT | pdb_00003wkt

Complex structure of an open form of NADPH-cytochrome P450 reductase and heme oxygenase-1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Heme oxygenase-like	8035972	3001676	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Heme oxygenase-like	8035972	3001676	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Riboflavin synthase domain-like	8034256	3001812	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Flavoproteins	8034257	3001217	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ferredoxin reductase-like, C-terminal NADP-linked domain	8034259	3001461	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Riboflavin synthase domain-like	8034256	3001812	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ferredoxin reductase-like, C-terminal NADP-linked domain	8034259	3001461	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Flavoproteins	8034257	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)
D	Chalcone_N	e3wktD1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: Chalcone_N	ECOD (develop294)
C	NiFe_hyd_SSU_C	e3wktC1	A: alpha bundles	X: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	F: NiFe_hyd_SSU_C	ECOD (develop294)
B	Chalcone_N	e3wktB2	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: Chalcone_N	ECOD (develop294)
B	V-set	e3wktB8	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: V-set	ECOD (develop294)
A	NiFe_hyd_SSU_C	e3wktA3	A: alpha bundles	X: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	F: NiFe_hyd_SSU_C	ECOD (develop294)
A	V-set	e3wktA5	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: V-set	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF01126	Heme oxygenase (Heme_oxygenase)	Heme oxygenase		Domain
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
C, D	Heme oxygenase 1	cation binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding oxidoreductase activity monooxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen arachidonate omega-hydroxylase activity catalytic activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen phosphoric ester hydrolase activity cation binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding oxidoreductase activity monooxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen arachidonate omega-hydroxylase activity catalytic activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen phosphoric ester hydrolase activity phospholipase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity glycerophospholipase activity hydrolase activity D-type glycerophospholipase activity lipase activity heme oxygenase (decyclizing) activity protein homodimerization activity protein dimerization activity tetrapyrrole binding heme binding structural molecule activity enzyme binding	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis response to stimulus response to chemical response to xenobiotic stimulus cellular response to stimulus intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis response to stimulus response to chemical response to xenobiotic stimulus cellular response to stimulus cellular response to nutrient levels response to nutrient levels cellular response to chemical stimulus response to nutrient cellular response to nutrient cellular process heme metabolic process pigment metabolic process catabolic process heme oxidation tetrapyrrole metabolic process porphyrin-containing compound catabolic process metabolic process porphyrin-containing compound metabolic process tetrapyrrole catabolic process multicellular organismal process system process circulatory system process regulation of blood pressure biological regulation regulation of biological quality blood circulation positive regulation of epithelial cell apoptotic process regulation of biological process positive regulation of programmed cell death regulation of cellular process regulation of epithelial cell apoptotic process regulation of apoptotic process positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process epithelial cell apoptotic process apoptotic process programmed cell death positive regulation of cellular process regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis positive regulation of cell population proliferation endothelial cell proliferation angiogenesis multicellular organism development tube morphogenesis positive regulation of endothelial cell proliferation anatomical structure development epithelial cell proliferation blood vessel development system development developmental process positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis cell population proliferation blood vessel morphogenesis tube development blood vessel endothelial cell proliferation involved in sprouting angiogenesis positive regulation of epithelial cell proliferation sprouting angiogenesis vasculature development circulatory system development anatomical structure morphogenesis regulation of endothelial cell proliferation regulation of cell population proliferation anatomical structure formation involved in morphogenesis regulation of epithelial cell proliferation cellular response to heat cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus extrinsic apoptotic signaling pathway via death domain receptors signaling negative regulation of signaling negative regulation of biological process regulation of signal transduction extrinsic apoptotic signaling pathway negative regulation of cell communication cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of cellular process signal transduction regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death negative regulation of extrinsic apoptotic signaling pathway via death domain receptors negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of response to stimulus regulation of extrinsic apoptotic signaling pathway via death domain receptors regulation of cell communication regulation of apoptotic signaling pathway regulation of immune effector process negative regulation of mast cell cytokine production cytokine production regulation of cytokine production mast cell cytokine production regulation of immune system process regulation of multicellular organismal process myeloid leukocyte cytokine production cytokine production involved in immune response negative regulation of macromolecule metabolic process production of molecular mediator of immune response regulation of biosynthetic process negative regulation of cytokine production involved in immune response regulation of cytokine production involved in immune response regulation of mast cell cytokine production immune response negative regulation of metabolic process negative regulation of immune effector process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process immune effector process regulation of gene expression negative regulation of production of molecular mediator of immune response negative regulation of gene expression biosynthetic process negative regulation of immune system process negative regulation of biosynthetic process immune system process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response negative regulation of multicellular organismal process regulation of metabolic process multicellular organismal-level iron ion homeostasis multicellular organismal-level homeostasis multicellular organismal-level chemical homeostasis negative regulation of viral process regulation of viral process regulation of viral life cycle negative regulation of viral life cycle viral process viral life cycle wound healing wound healing involved in inflammatory response defense response inflammatory response to wounding inflammatory response response to wounding pigment catabolic process heme catabolic process cellular response to arsenic-containing substance response to arsenic-containing substance regulation of smooth muscle cell proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation muscle cell proliferation response to decreased oxygen levels response to hypoxia response to oxygen levels cellular developmental process hemopoiesis cell development erythrocyte differentiation myeloid cell differentiation cell differentiation homeostasis of number of cells myeloid cell homeostasis erythrocyte homeostasis biological process involved in interspecies interaction between organisms host-mediated suppression of viral proces host-mediated perturbation of viral transcription host-mediated suppression of viral transcription host-mediated perturbation of viral process modulation of process of another organism host-mediated perturbation of symbiont process cellular response to metal ion response to metal ion cellular response to cadmium ion response to cadmium ion response to polycyclic arene response to 3-methylcholanthrene response to hydrogen peroxide response to oxidative stress response to oxygen-containing compound response to reactive oxygen species negative regulation of epithelial cell apoptotic process regulation of vascular associated smooth muscle cell proliferation negative regulation of cell population proliferation negative regulation of vascular associated smooth muscle cell proliferation negative regulation of smooth muscle cell proliferation vascular associated smooth muscle cell proliferation positive regulation of locomotion regulation of cell motility cell migration involved in sprouting angiogenesis regulation of blood vessel endothelial cell migration endothelial cell migration positive regulation of cell migration positive regulation of cell motility regulation of cell migration blood vessel endothelial cell migration regulation of endothelial cell migration cell migration positive regulation of cell migration involved in sprouting angiogenesis cell motility locomotion regulation of cell migration involved in sprouting angiogenesis positive regulation of blood vessel endothelial cell migration regulation of locomotion positive regulation of endothelial cell migration phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process primary metabolic process phosphorus metabolic process lipid metabolic process response to hormone response to endogenous stimulus response to estrogen response to cisplatin cellular response to cisplatin negative regulation of catabolic process macroautophagy autophagy regulation of catabolic process regulation of autophagy negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy process utilizing autophagic mechanism gland development animal organ development animal organ regeneration liver development regeneration hepaticobiliary system development liver regeneration neuron apoptotic process negative regulation of neuron apoptotic process regulation of neuron apoptotic process response to lipid response to fatty acid response to arachidonate negative regulation of ferroptosis regulation of ferroptosis ferroptosis intracellular signal transduction DNA damage response intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway positive regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process positive regulation of macroautophagy establishment of organelle localization regulation of localization regulation of myeloid leukocyte mediated immunity regulated exocytosis negative regulation of transport cell activation involved in immune response leukocyte degranulation myeloid leukocyte mediated immunity vesicle-mediated transport myeloid leukocyte activation localization negative regulation of secretion establishment of localization in cell leukocyte mediated immunity negative regulation of secretion by cell negative regulation of myeloid leukocyte mediated immunity vacuolar localization establishment of localization mast cell degranulation regulation of secretion regulation of leukocyte mediated immunity exocytosis lysosome localization cellular localization transport negative regulation of regulated secretory pathway negative regulation of leukocyte degranulation regulation of mast cell degranulation leukocyte activation regulation of regulated secretory pathway secretion by cell regulation of secretion by cell negative regulation of exocytosis organelle localization leukocyte activation involved in immune response negative regulation of mast cell degranulation mast cell activation regulation of leukocyte degranulation mast cell mediated immunity secretion regulation of transport cell activation export from cell regulation of vesicle-mediated transport myeloid cell activation involved in immune response mast cell activation involved in immune response regulation of exocytosis negative regulation of leukocyte mediated immunity regulation of developmental process regulation of vasculature development positive regulation of developmental process regulation of anatomical structure morphogenesis regulation of multicellular organismal development positive regulation of angiogenesis positive regulation of vasculature development regulation of angiogenesis positive regulation of multicellular organismal process muscle cell apoptotic process regulation of muscle cell apoptotic process negative regulation of muscle cell apoptotic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription response to nicotine small GTPase-mediated signal transduction intracellular signaling cassette regulation of cytokine production involved in inflammatory response negative regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response cytokine production involved in inflammatory response	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm membrane microdomain cell periphery membrane raft plasma membrane raft membrane plasma membrane plasma membrane region caveola membrane-bounded organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm membrane microdomain cell periphery membrane raft plasma membrane raft membrane plasma membrane plasma membrane region caveola membrane-bounded organelle organelle subcompartment intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane nucleus
A, B	NADPH-cytochrome P450 reductase	oxidoreductase activity catalytic activity 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 cytochrome-b5 reductase activity, acting on NAD(P)H oxidoreductase activity catalytic activity 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 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 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 cellular response to gonadotropin stimulus response to gonadotropin 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 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 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 intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle organelle subcompartment membrane intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle organelle subcompartment membrane intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle 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
C, D	IPR002051	Haem oxygenase	Family
C, D	IPR016084	Haem oxygenase-like, multi-helical	Homologous Superfamily
C, D	IPR018207	Haem oxygenase conserved site	Conserved Site
C, D	IPR016053	Haem oxygenase-like	Family
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

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.