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Yorodumi- PDB-8uft: Structure of human endothelial nitric oxide synthase P370N mutant... -
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-Basic information
Entry | Database: PDB / ID: 8uft | ||||||
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Title | Structure of human endothelial nitric oxide synthase P370N mutant heme domain in complex with 4-methyl-7-(4-methyl-2,3,4,5-tetrahydrobenzo[f][1,4]oxazepin-7-yl)quinolin-2-amine | ||||||
Components | Nitric oxide synthase 3 | ||||||
Keywords | OXIDOREDUCTASE / nitric oxide synthase inhibitor / heme enzyme | ||||||
Function / homology | Function and homology information regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / NOSTRIN mediated eNOS trafficking / negative regulation of muscle hyperplasia / smooth muscle hyperplasia / regulation of nervous system process / ovulation from ovarian follicle / response to fluid shear stress / pulmonary valve morphogenesis / negative regulation of biomineral tissue development ...regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / NOSTRIN mediated eNOS trafficking / negative regulation of muscle hyperplasia / smooth muscle hyperplasia / regulation of nervous system process / ovulation from ovarian follicle / response to fluid shear stress / pulmonary valve morphogenesis / negative regulation of biomineral tissue development / positive regulation of guanylate cyclase activity / Nitric oxide stimulates guanylate cyclase / regulation of systemic arterial blood pressure by endothelin / ROS and RNS production in phagocytes / tetrahydrobiopterin binding / arginine binding / aortic valve morphogenesis / endocardial cushion morphogenesis / positive regulation of Notch signaling pathway / ventricular septum morphogenesis / cadmium ion binding / negative regulation of potassium ion transport / negative regulation of calcium ion transport / actin monomer binding / negative regulation of platelet activation / blood vessel remodeling / endothelial cell migration / nitric-oxide synthase (NADPH) / positive regulation of blood vessel endothelial cell migration / nitric oxide mediated signal transduction / nitric-oxide synthase activity / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / eNOS activation / arginine catabolic process / regulation of sodium ion transport / lipopolysaccharide-mediated signaling pathway / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / homeostasis of number of cells within a tissue / nitric oxide biosynthetic process / negative regulation of blood pressure / response to hormone / removal of superoxide radicals / blood vessel diameter maintenance / cell redox homeostasis / VEGFR2 mediated vascular permeability / mitochondrion organization / establishment of localization in cell / lung development / negative regulation of smooth muscle cell proliferation / potassium ion transport / caveola / regulation of blood pressure / vasodilation / positive regulation of angiogenesis / calcium ion transport / endocytic vesicle membrane / FMN binding / flavin adenine dinucleotide binding / NADP binding / response to heat / scaffold protein binding / angiogenesis / in utero embryonic development / response to lipopolysaccharide / Extra-nuclear estrogen signaling / cytoskeleton / calmodulin binding / negative regulation of cell population proliferation / Golgi membrane / heme binding / positive regulation of gene expression / Golgi apparatus / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.78 Å | ||||||
Authors | Li, H. / Poulos, T.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2024 Title: Crystallographic and Computational Insights into Isoform-Selective Dynamics in Nitric Oxide Synthase. Authors: Li, H. / Hardy, C.D. / Reidl, C.T. / Jing, Q. / Xue, F. / Cinelli, M. / Silverman, R.B. / Poulos, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8uft.cif.gz | 695.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8uft.ent.gz | 572.5 KB | Display | PDB format |
PDBx/mmJSON format | 8uft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8uft_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 8uft_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 8uft_validation.xml.gz | 76.9 KB | Display | |
Data in CIF | 8uft_validation.cif.gz | 109 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/8uft ftp://data.pdbj.org/pub/pdb/validation_reports/uf/8uft | HTTPS FTP |
-Related structure data
Related structure data | 8ufpC 8ufqC 8ufrC 8ufsC 8ufuC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 49362.758 Da / Num. of mol.: 4 / Mutation: P370N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: endothelial / Gene: NOS3 / Plasmid: pCWori / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29474, nitric-oxide synthase (NADPH) |
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-Non-polymers , 11 types, 1365 molecules
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-H4B / #4: Chemical | ChemComp-WK2 / ( Mass: 319.400 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H21N3O / Feature type: SUBJECT OF INVESTIGATION #5: Chemical | ChemComp-ACT / #6: Chemical | ChemComp-BTB / #7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-CL / #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-GD / #12: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 8-10% PEG3350, 0.1M BIS-TRIS 0.2-0.3M MG ACETATE, 0.1M GDCL3 10% GLYCEROL, 5 MM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 12, 2023 / Details: mirrors |
Radiation | Monochromator: DOUBLE CRYSTAL SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→40.02 Å / Num. obs: 186583 / % possible obs: 98.8 % / Redundancy: 4.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.06 / Rrim(I) all: 0.133 / Χ2: 0.9 / Net I/σ(I): 9 / Num. measured all: 871466 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 4.3 % / Rmerge(I) obs: 2.086 / Num. unique obs: 9137 / CC1/2: 0.488 / Rpim(I) all: 1.088 / Rrim(I) all: 2.361 / Χ2: 0.86 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.78→40.016 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.41 / Phase error: 23.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→40.016 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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