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Yorodumi- PDB-3jwy: Structure of endothelial nitric oxide synthase heme domain comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jwy | ||||||
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Title | Structure of endothelial nitric oxide synthase heme domain complexed with N1-{(3'R,4'S)-4'-[(6"-amino-4"-methylpyridin-2"-yl)methyl]pyrrolidin-3'-yl}-N2-(3'-fluorophenethyl)ethane-1,2-diamine tetrahydrochloride | ||||||
Components | Nitric oxide synthase, endothelial | ||||||
Keywords | OXIDOREDUCTASE / heme enzyme / substrate inhibitor | ||||||
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 synthase activity / nitric oxide mediated signal transduction / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / mitochondrion organization / 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 synthase activity / nitric oxide mediated signal transduction / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / mitochondrion organization / negative regulation of blood pressure / nitric oxide biosynthetic process / response to hormone / 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 | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.24 Å | ||||||
Authors | Delker, S.L. / Li, H. / Poulos, T.L. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Unexpected binding modes of nitric oxide synthase inhibitors effective in the prevention of a cerebral palsy phenotype in an animal model. Authors: Delker, S.L. / Ji, H. / Li, H. / Jamal, J. / Fang, J. / Xue, F. / 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 | 3jwy.cif.gz | 298.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jwy.ent.gz | 232.4 KB | Display | PDB format |
PDBx/mmJSON format | 3jwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/3jwy ftp://data.pdbj.org/pub/pdb/validation_reports/jw/3jwy | HTTPS FTP |
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-Related structure data
Related structure data | 3jwsC 3jwtC 3jwuC 3jwvC 3jwwC 3jwxC 3jwzC 3jx0C 3jx1C 3jx2C 3jx3C 3jx4C 3jx5C 3jx6C 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 49710.105 Da / Num. of mol.: 2 / Fragment: Residues 39-482 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 , 8 types, 430 molecules
#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 DIMETHYL ARSENIC MOIETY IS DERIVED FROM CACODYLATE WHEN IT REACTS WITH SURFACE CYSTEINE RESIDUE ...THE DIMETHYL ARSENIC MOIETY IS DERIVED FROM CACODYLATE |
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Sequence details | ARG 100 IS A SEQUENCE VARIANT AS LISTED IN UNP ENTRY P29473 (AAA30669) |
-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: 49.88 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 3350, magnesium acetate, sodium cacodylate, 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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 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: 2.24→44.2 Å / Num. obs: 47798 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.24→2.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.59 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.24→44.2 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.155 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.195 / 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: 36.113 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→44.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.24→2.3 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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