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Yorodumi- PDB-5fvz: Structure of bovine endothelial nitric oxide synthase heme domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fvz | ||||||
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Title | Structure of bovine endothelial nitric oxide synthase heme domain in complex with 6-(2-(5-(3-(dimethylamino)propyl)pyridin-3-yl)ethyl)-4-methylpyridin-2-amine | ||||||
Components | ENDOTHELIAL NITRIC OXIDE SYNTHASE | ||||||
Keywords | OXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / 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 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 / OTHER / Resolution: 2.048 Å | ||||||
Authors | Li, H. / Poulos, T.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fvz.cif.gz | 342.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fvz.ent.gz | 289.6 KB | Display | PDB format |
PDBx/mmJSON format | 5fvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/5fvz ftp://data.pdbj.org/pub/pdb/validation_reports/fv/5fvz | HTTPS FTP |
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-Related structure data
Related structure data | 5fvoC 5fvpC 5fvqC 5fvrC 5fvsC 5fvtC 5fvuC 5fvvC 5fvwC 5fvxC 5fvyC 5fw0C 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: 49727.012 Da / Num. of mol.: 2 / Fragment: HEME DOMAIN, RESIDUES 40-482 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / 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, 491 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ZN / | #7: Chemical | #8: 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.7 % Description: OVERALL RMERGE 0.110 RPIM 0.062 CC ONE HALF 0.995 HIGHEST RESOLUTION SHELL RMERGE 1.624 RPIM 0.925 CC ONE HALF 0.359 |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.181 |
Detector | Type: MARRESEARCH MAR324 / Detector: CCD / Date: Dec 16, 2015 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.181 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 61917 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 36.13 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.05→2.13 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.5 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.048→39.191 Å / SU ML: 0.27 / σ(F): 0.15 / Phase error: 23.96 / Stereochemistry target values: ML
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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: 42.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.048→39.191 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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