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Yorodumi- PDB-5uo8: Structure of human endothelial nitric oxide synthase heme domain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uo8 | ||||||
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Title | Structure of human endothelial nitric oxide synthase heme domain in complex with 3-[(2-aminoquinolin-7-yl)methoxy]-5-((methylamino)methyl)benzonitrile | ||||||
Components | Nitric oxide synthase, endothelial | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / nitric / oxide / synthase / inhibitor / complex / heme / enzyme / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
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 / 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 / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of sodium ion transport / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / lipopolysaccharide-mediated signaling pathway / homeostasis of number of cells within a tissue / nitric oxide biosynthetic process / negative regulation of blood pressure / removal of superoxide radicals / blood vessel diameter maintenance / potassium ion transport / negative regulation of smooth muscle cell proliferation / lung development / VEGFR2 mediated vascular permeability / response to hormone / cell redox homeostasis / mitochondrion organization / caveola / establishment of localization in cell / 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 / Extra-nuclear estrogen signaling / response to lipopolysaccharide / calmodulin binding / cytoskeleton / Golgi membrane / negative regulation of cell population proliferation / heme binding / positive regulation of gene expression / Golgi apparatus / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||
Authors | Chreifi, G. / Li, H. / Poulos, T.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Med. Chem. / Year: 2017 Title: Nitrile in the Hole: Discovery of a Small Auxiliary Pocket in Neuronal Nitric Oxide Synthase Leading to the Development of Potent and Selective 2-Aminoquinoline Inhibitors. Authors: Cinelli, M.A. / Li, H. / Chreifi, G. / Poulos, T.L. / Silverman, R.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uo8.cif.gz | 673.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uo8.ent.gz | 559.7 KB | Display | PDB format |
PDBx/mmJSON format | 5uo8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uo8_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 5uo8_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 5uo8_validation.xml.gz | 66.1 KB | Display | |
Data in CIF | 5uo8_validation.cif.gz | 87.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/5uo8 ftp://data.pdbj.org/pub/pdb/validation_reports/uo/5uo8 | HTTPS FTP |
-Related structure data
Related structure data | 5unrC 5unsC 5untC 5unuC 5unvC 5unwC 5unxC 5unyC 5unzC 5uo0C 5uo1C 5uo2C 5uo3C 5uo4C 5uo5C 5uo6C 5uo7C 5uo9C 5uoaC 5uobC 5uocC 5uodC 4d1pS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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: 49345.770 Da / Num. of mol.: 4 / Fragment: UNP residues 41-480 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NOS3 / Organ: endothelial / Plasmid: pCWori / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29474, nitric-oxide synthase (NADPH) |
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-Non-polymers , 8 types, 353 molecules
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-H4B / #4: Chemical | ChemComp-8EV / #5: Chemical | ChemComp-BTB / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-GD / #9: Water | ChemComp-HOH / | |
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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: 2.69 Å3/Da / Density % sol: 54.3 % / Description: rice grain-like |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 12-15% PEG3350, 0.1 M Bis-Tris, 0.2-0.3 M magnesium acetate, 0.1 M gadolinium chloride, 10% glycerol, 5 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2016 / Details: mirrors |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→60 Å / Num. obs: 90391 / % possible obs: 90.4 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / CC1/2: 0.986 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.154 / Rsym value: 0.154 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.18→2.24 Å / Redundancy: 2.8 % / Rmerge(I) obs: 1.975 / Mean I/σ(I) obs: 1.2 / Num. unique all: 4538 / CC1/2: 0.368 / Rpim(I) all: 1.969 / Rsym value: 1.975 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4D1P Resolution: 2.18→49.535 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.18→49.535 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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