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Yorodumi- PDB-4luw: Structure of bovine endothelial nitric oxide synthase heme domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4luw | ||||||
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Title | Structure of bovine endothelial nitric oxide synthase heme domain in complex with 6-((((3R,5S)-5-(((6-amino-4-methylpyridin-2-yl)methoxy)methyl)pyrrolidin-3-yl)oxy)methyl)-4-methylpyridin-2-amine | ||||||
Components | Nitric oxide synthase, endothelial | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / nitric oxide synthase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / calmodulin binding / cytoskeleton / heme binding / Golgi apparatus / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å | ||||||
Authors | Li, H. / Poulos, T.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structural and biological studies on bacterial nitric oxide synthase inhibitors. Authors: Holden, J.K. / Li, H. / Jing, Q. / Kang, S. / Richo, J. / 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 | 4luw.cif.gz | 344.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4luw.ent.gz | 278.7 KB | Display | PDB format |
PDBx/mmJSON format | 4luw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4luw_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4luw_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4luw_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 4luw_validation.cif.gz | 49.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/4luw ftp://data.pdbj.org/pub/pdb/validation_reports/lu/4luw | HTTPS FTP |
-Related structure data
Related structure data | 4luxC 4lwaC 4lwbC 1nseS 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 49569.820 Da / Num. of mol.: 2 / Fragment: UNP residues 41-482 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: NOS3 / Plasmid: pCWori / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29473, nitric-oxide synthase (NADPH) |
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-Non-polymers , 7 types, 309 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ACT / #6: Chemical | #7: Chemical | ChemComp-ZN / | #8: 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: 2.45 Å3/Da / Density % sol: 49.89 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 18-20% PEG3350, 0.1 M cacodylate, 0.2 M magnesium acetate, 5 mM TCEP, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.097 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2011 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.097 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 46657 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.613 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTYR 1NSE Resolution: 2.25→44.07 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 13.846 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.275 / ESU R Free: 0.212 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 43.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→44.07 Å
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