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- PDB-5fvy: 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: 5fvy | ||||||
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Title | Structure of bovine endothelial nitric oxide synthase heme domain in complex with 4-methyl-6-(2-(5-(4-methylpiperazin-1-yl)pyridin-3-yl) ethyl)pyridin-2-amine | ||||||
![]() | NITRIC OXIDE SYNTHASE, ENDOTHELIAL | ||||||
![]() | OXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / INHIBITOR COMPLEX | ||||||
Function / homology | ![]() cellular response to laminar fluid shear stress / positive regulation of guanylate cyclase activity / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / nitric oxide mediated signal transduction / nitric-oxide synthase activity / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric oxide biosynthetic process / negative regulation of blood pressure ...cellular response to laminar fluid shear stress / positive regulation of guanylate cyclase activity / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / nitric oxide mediated signal transduction / nitric-oxide synthase activity / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric oxide biosynthetic process / negative regulation of blood pressure / mitochondrion organization / response to hormone / caveola / blood coagulation / FMN binding / NADP binding / flavin adenine dinucleotide binding / response to lipopolysaccharide / cytoskeleton / calmodulin binding / heme binding / Golgi apparatus / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Li, H. / Poulos, T.L. | ||||||
![]() | ![]() Title: Potent and Selective Human Neuronal Nitric Oxide Synthase Inhibition by Optimization of the 2-Aminopyridine-Based Scaffold with a Pyridine Linker. Authors: Wang, H. / Qin, Y. / Li, H. / 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 | ![]() | 342.2 KB | Display | ![]() |
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PDB format | ![]() | 289.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 35.2 KB | Display | |
Data in CIF | ![]() | 49.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fvoC ![]() 5fvpC ![]() 5fvqC ![]() 5fvrC ![]() 5fvsC ![]() 5fvtC ![]() 5fvuC ![]() 5fvvC ![]() 5fvwC ![]() 5fvxC ![]() 5fvzC ![]() 5fw0C 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: HEME DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 8 types, 366 molecules ![](data/chem/img/HEM.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/H4B.gif)
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![](data/chem/img/ACT.gif)
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![](data/chem/img/GOL.gif)
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#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ACT / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-ZN / | #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUE 100 IS FOUND AS AN ARG IN STRUCTURE BUT IS A CYS IN DATABASE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.7 % Description: OVERALL RMERGE 0.136 RPIM 0.051 CC ONE HALF 0.997 HIGHEST RESOLUTION SHELL RMERGE 1.722 RPIM 0.929 CC ONE HALF 0.324 |
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Crystal grow | pH: 6 Details: 20-22% PEG3350 0.1M CACODYLATE, PH6.0 140-200 MM MG ACETATE 5 MM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2015 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 57071 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 36.84 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.1→2.19 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.9 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.098→87.847 Å / SU ML: 0.28 / σ(F): 0.06 / Phase error: 23.86 / Stereochemistry target values: ML Details: RESIDUES 109 TO 119 IN CHAIN A AND 111 TO 120 IN CHAIN B ARE DISORDERED.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.098→87.847 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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