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- PDB-3nlf: Structure of endothelial nitric oxide synthase heme domain comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nlf | ||||||
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Title | Structure of endothelial nitric oxide synthase heme domain complexed with 6-{{(3'R,4'S)-3'-[2"-(3'''-fluorophenethylamino)ethoxy]pyrrolidin-4'-yl}methyl}-4-methylpyridin-2-amine | ||||||
![]() | Nitric oxide synthase, endothelial | ||||||
![]() | OXIDOREDUCTASE / nitric oxide synthase / heme enzyme / substrate inhibitor | ||||||
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 / response to hormone / mitochondrion organization / 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 | ![]() ![]() ![]() | ||||||
![]() | Ji, H. / Delker, S.L. / Li, H. / Martasek, P. / Roman, L. / Poulos, T.L. / Silverman, R.B. | ||||||
![]() | ![]() Title: Exploration of the Active Site of Neuronal Nitric Oxide Synthase by the Design and Synthesis of Pyrrolidinomethyl 2-Aminopyridine Derivatives. Authors: Ji, H. / Delker, S.L. / Li, H. / Martasek, P. / Roman, L.J. / 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 | ![]() | 297 KB | Display | ![]() |
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PDB format | ![]() | 231.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3nldC ![]() 3nleC ![]() 3nlgC ![]() 3nlhC ![]() 3nliC ![]() 3nljC ![]() 3nlkC ![]() 3nlmC ![]() 3nlnC ![]() 3nloC ![]() 3nlpC ![]() 3nlqC ![]() 3nlrC 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: 49710.105 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 39-482 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 8 types, 346 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/H4B.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/JRS.gif)
![](data/chem/img/CAD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/H4B.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/JRS.gif)
![](data/chem/img/CAD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-ZN / | #9: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE HETNAM OF LIGAND JRS IS BASED ON IUPAC NOMENCLATURE WHILE THE NAME IN THE TITLE HAS BEEN ...THE HETNAM OF LIGAND JRS IS BASED ON IUPAC NOMENCLATU |
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Sequence details | CYS TO ARG CONFLICT IN UNP ENTRY P29473 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.02 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 9-12% PEG 3350, 0.2M magnesium acetate, 0.1M sodium cacodylate, 0.005M TCEP-HCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 20, 2008 / 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: 2.32→50 Å / Num. obs: 43117 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 2.32→2.36 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2109 / Rsym value: 0.331 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.674 Å2
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Refinement step | Cycle: LAST / Resolution: 2.32→38.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.32→2.38 Å / Total num. of bins used: 20
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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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