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- PDB-6av6: Structure of human endothelial nitric oxide synthase heme domain ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6av6 | ||||||
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Title | Structure of human endothelial nitric oxide synthase heme domain in complex with 6-(3-Fluoro-5-(3-(methylamino)propyl)phenethyl)-4-methylpyridin-2-amine | ||||||
![]() | Nitric oxide synthase, endothelial | ||||||
![]() | OXIDOREDUCTASE / nitric oxide synthase inhibitor complex heme enzyme | ||||||
Function / homology | ![]() regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / NOSTRIN mediated eNOS trafficking / negative regulation of muscle hyperplasia / regulation of nervous system process / smooth muscle hyperplasia / response to fluid shear stress / ovulation from ovarian follicle / 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 / regulation of nervous system process / smooth muscle hyperplasia / response to fluid shear stress / ovulation from ovarian follicle / 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 / aortic valve morphogenesis / arginine binding / endocardial cushion morphogenesis / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / cadmium ion binding / negative regulation of potassium ion transport / negative regulation of calcium ion transport / actin monomer binding / negative regulation of platelet activation / endothelial cell migration / nitric-oxide synthase (NADPH) / positive regulation of blood vessel endothelial cell migration / blood vessel remodeling / nitric oxide mediated signal transduction / nitric-oxide synthase activity / eNOS activation / arginine catabolic process / regulation of sodium ion transport / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / homeostasis of number of cells within a tissue / lipopolysaccharide-mediated signaling pathway / nitric oxide biosynthetic process / negative regulation of blood pressure / removal of superoxide radicals / blood vessel diameter maintenance / mitochondrion organization / VEGFR2 mediated vascular permeability / response to hormone / cell redox homeostasis / caveola / establishment of localization in cell / negative regulation of smooth muscle cell proliferation / lung development / potassium ion transport / regulation of blood pressure / vasodilation / positive regulation of angiogenesis / calcium ion transport / endocytic vesicle membrane / FMN binding / NADP binding / flavin adenine dinucleotide 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, H. / Poulos, T.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Improvement of Cell Permeability of Human Neuronal Nitric Oxide Synthase Inhibitors Using Potent and Selective 2-Aminopyridine-Based Scaffolds with a Fluorobenzene Linker. Authors: Do, H.T. / Wang, H.Y. / Li, H. / Chreifi, G. / Poulos, T.L. / Silverman, R.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 676.9 KB | Display | ![]() |
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PDB format | ![]() | 562.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 66.4 KB | Display | |
Data in CIF | ![]() | 87.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6auqC ![]() 6aurC ![]() 6ausC ![]() 6autC ![]() 6auuC ![]() 6auvC ![]() 6auwC ![]() 6auxC ![]() 6auyC ![]() 6auzC ![]() 6av0C ![]() 6av1C ![]() 6av2C ![]() 6av3C ![]() 6av4C ![]() 6av5C ![]() 6av7C ![]() 4dipS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 49345.770 Da / Num. of mol.: 4 / Fragment: UNP residues 41-480 Source method: isolated from a genetically manipulated source Details: Residues 108 to 119 are disordered. The N-terminal residues 41 to 67 are invisible in density. Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 9 types, 359 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/W68.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GD.gif)
![](data/chem/img/H4B.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/W68.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GD.gif)
![](data/chem/img/H4B.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-W68 / #4: Chemical | ChemComp-BTB / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-CL / #8: Chemical | ChemComp-GD / #9: Chemical | ChemComp-H4B / #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.3 % / Description: rod |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 12-15% 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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 19, 2016 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→50 Å / Num. obs: 116007 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.169 / Rsym value: 0.169 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.08→2.13 Å / Redundancy: 5.5 % / Rmerge(I) obs: 2.916 / Num. unique obs: 5716 / CC1/2: 0.623 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DIP Resolution: 2.08→39.131 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.88 / 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: 2.08→39.131 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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