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Yorodumi- PDB-6cif: Structure of the human endothelial nitric oxide synthase heme dom... -
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-Basic information
Entry | Database: PDB / ID: 6cif | ||||||
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Title | Structure of the human endothelial nitric oxide synthase heme domain in complex with N-(1-(Piperidin-4-yl)indolin-5-yl)thiophene-2-carboximidamide | ||||||
Components | Nitric oxide synthase, endothelial | ||||||
Keywords | OXIDOREDUCTASE / nitric oxide synthase inhibitor complex 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 / 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 platelet activation / negative regulation of calcium ion transport / actin monomer binding / endothelial cell migration / removal of superoxide radicals / nitric-oxide synthase (NADPH) / positive regulation of blood vessel endothelial cell migration / blood vessel remodeling / nitric-oxide synthase activity / eNOS activation / nitric oxide mediated signal transduction / arginine catabolic process / homeostasis of number of cells within a tissue / regulation of sodium ion transport / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / lipopolysaccharide-mediated signaling pathway / nitric oxide biosynthetic process / negative regulation of blood pressure / blood vessel diameter maintenance / mitochondrion organization / response to hormone / cell redox homeostasis / VEGFR2 mediated vascular permeability / caveola / negative regulation of smooth muscle cell proliferation / establishment of localization in cell / lung development / potassium ion transport / regulation of blood pressure / vasodilation / endocytic vesicle membrane / positive regulation of angiogenesis / calcium ion transport / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Chreifi, G. / Li, H. / Poulos, T.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2018 Title: Structural Basis for Isoform Selective Nitric Oxide Synthase Inhibition by Thiophene-2-carboximidamides. Authors: Li, H. / Evenson, R.J. / Chreifi, G. / 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 | 6cif.cif.gz | 702.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cif.ent.gz | 580.3 KB | Display | PDB format |
PDBx/mmJSON format | 6cif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/6cif ftp://data.pdbj.org/pub/pdb/validation_reports/ci/6cif | HTTPS FTP |
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-Related structure data
Related structure data | 6cicC 6cidC 6cieC 4dipS S: Starting model for refinement C: citing same article (ref.) |
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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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: endothelial / Gene: NOS3 / Plasmid: pCWori / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29474, nitric-oxide synthase (NADPH) |
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-Non-polymers , 9 types, 600 molecules
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-H4B / #4: Chemical | ChemComp-F2J / #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: 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: rods |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 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: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2017 / 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: 2.2→50 Å / Num. obs: 94161 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.154 / Rsym value: 0.212 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 4.8 % / Rmerge(I) obs: 2.798 / Num. unique obs: 4645 / CC1/2: 0.231 / Rpim(I) all: 2.093 / Rsym value: 2.798 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DIP Resolution: 2.2→46.065 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 27.89 / 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: 2.2→46.065 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -49.3201 Å / Origin y: -0.0703 Å / Origin z: -190.2025 Å
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Refinement TLS group | Selection details: all |