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- PDB-5vvd: 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: 5vvd | ||||||
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Title | Structure of human endothelial nitric oxide synthase heme domain in complex with 4-(2-(((2-Amino-4-methylquinolin-7-yl)methyl)amino)ethyl)benzonitrile | ||||||
![]() | Nitric oxide synthase, endothelial | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / nitric oxide synthase inhibitor complex / heme enzyme / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
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: Hydrophilic, Potent, and Selective 7-Substituted 2-Aminoquinolines as Improved Human Neuronal Nitric Oxide Synthase Inhibitors. Authors: Pensa, A.V. / Cinelli, M.A. / Li, H. / Chreifi, G. / Mukherjee, P. / Roman, L.J. / Martasek, P. / 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 | ![]() | 678.3 KB | Display | ![]() |
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PDB format | ![]() | 565.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 64.6 KB | Display | |
Data in CIF | ![]() | 84.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vuiC ![]() 5vujC ![]() 5vukC ![]() 5vulC ![]() 5vumC ![]() 5vunC ![]() 5vuoC ![]() 5vupC ![]() 5vuqC ![]() 5vurC ![]() 5vusC ![]() 5vutC ![]() 5vuuC ![]() 5vuvC ![]() 5vuwC ![]() 5vuxC ![]() 5vuyC ![]() 5vuzC ![]() 5vv0C ![]() 5vv1C ![]() 5vv2C ![]() 5vv3C ![]() 5vv4C ![]() 5vv5C ![]() 5vv6C ![]() 5vv7C ![]() 5vv8C ![]() 5vv9C ![]() 5vvaC ![]() 5vvbC ![]() 5vvcC ![]() 5vvgC ![]() 5vvnC ![]() 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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2 | ![]()
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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: residues 41-480 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 9 types, 124 molecules ![](data/chem/img/HEM.gif)
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![](data/chem/img/BTB.gif)
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![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-H4B / #4: Chemical | ChemComp-9OG / #5: Chemical | ChemComp-BTB / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-CL / #9: Chemical | ChemComp-GD / #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: rice grain |
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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 S 6M / Detector: PIXEL / Date: Feb 27, 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: 2.19→50 Å / Num. obs: 97368 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.073 / Rsym value: 0.109 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.19→2.25 Å / Redundancy: 2.9 % / Rmerge(I) obs: 2.917 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4213 / CC1/2: 0.28 / Rpim(I) all: 2.009 / Rsym value: 2.917 / % possible all: 86.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DIP Resolution: 2.25→39.117 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 0.98 / Phase error: 36.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→39.117 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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