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- PDB-5vva: Structure of bovine endothelial nitric oxide synthase heme domain... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vva | ||||||
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Title | Structure of bovine endothelial nitric oxide synthase heme domain in complex with 4-(2-(((2-Amino-4-methylquinolin-7-yl)methyl)amino)ethyl)-2-methylbenzonitrile | ||||||
![]() | Nitric oxide synthase, endothelial | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / nitric oxide synthase / inhibitor complex / heme enzyme / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | ![]() positive regulation of guanylate cyclase activity / cellular response to laminar fluid shear stress / negative regulation of leukocyte cell-cell adhesion / nitric oxide mediated signal transduction / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / L-arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / response to hormone / negative regulation of blood pressure ...positive regulation of guanylate cyclase activity / cellular response to laminar fluid shear stress / negative regulation of leukocyte cell-cell adhesion / nitric oxide mediated signal transduction / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / L-arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / response to hormone / negative regulation of blood pressure / nitric oxide biosynthetic process / mitochondrion organization / caveola / blood coagulation / FMN binding / flavin adenine dinucleotide binding / NADP binding / response to lipopolysaccharide / cytoskeleton / calmodulin binding / heme binding / Golgi apparatus / metal ion binding / nucleus / plasma membrane / 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 | ![]() | 343.5 KB | Display | ![]() |
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PDB format | ![]() | 277.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 42.2 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 ![]() 5vvbC ![]() 5vvcC ![]() 5vvdC ![]() 5vvgC ![]() 5vvnC ![]() 1nseS S: Starting model for refinement C: citing same article ( |
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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, 2 molecules AB
#1: Protein | Mass: 49727.012 Da / Num. of mol.: 2 / Fragment: UNP residues 40-482 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 32 molecules 










#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ZN / | #7: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.8 % / Description: cube |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 20-24% PEG3350, 0.1 M cacodylate, 140-200 mM magnesium acetate, 5 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 16, 2015 / Details: mirrors |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.18 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→90 Å / Num. obs: 31268 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.077 / Rsym value: 0.085 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.55→2.73 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.288 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3658 / CC1/2: 0.276 / Rpim(I) all: 1.184 / Rsym value: 1.288 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1NSE Resolution: 2.55→87.542 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→87.542 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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