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Yorodumi- PDB-1vaf: Inducible nitric oxide synthase oxygenase domain complexed with t... -
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-Basic information
Entry | Database: PDB / ID: 1vaf | ||||||
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Title | Inducible nitric oxide synthase oxygenase domain complexed with the inhibitor AR-R17477 | ||||||
Components | Nitric oxide synthase, inducible | ||||||
Keywords | OXIDOREDUCTASE / MURINE INOSOXY INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / Peroxisomal protein import / cAMP-dependent protein kinase regulator activity / positive regulation of killing of cells of another organism / prostaglandin secretion / tetrahydrobiopterin binding / arginine binding / cortical cytoskeleton ...Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / Peroxisomal protein import / cAMP-dependent protein kinase regulator activity / positive regulation of killing of cells of another organism / prostaglandin secretion / tetrahydrobiopterin binding / arginine binding / cortical cytoskeleton / superoxide metabolic process / cGMP-mediated signaling / nitric-oxide synthase binding / peptidyl-cysteine S-nitrosylation / regulation of cytokine production involved in inflammatory response / cellular response to cytokine stimulus / regulation of insulin secretion / cellular response to organic cyclic compound / nitric-oxide synthase (NADPH) / blood vessel remodeling / nitric oxide mediated signal transduction / response to tumor necrosis factor / nitric-oxide synthase activity / arginine catabolic process / nitric oxide biosynthetic process / negative regulation of blood pressure / response to hormone / positive regulation of interleukin-8 production / negative regulation of protein catabolic process / response to bacterium / regulation of blood pressure / Hsp90 protein binding / circadian rhythm / cellular response to type II interferon / beta-catenin binding / positive regulation of interleukin-6 production / cellular response to xenobiotic stimulus / FMN binding / peroxisome / NADP binding / flavin adenine dinucleotide binding / actin binding / regulation of cell population proliferation / cellular response to lipopolysaccharide / response to lipopolysaccharide / calmodulin binding / response to hypoxia / intracellular signal transduction / defense response to bacterium / cadherin binding / inflammatory response / positive regulation of apoptotic process / negative regulation of gene expression / heme binding / protein kinase binding / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Fedorov, R. / Vasan, R. / Ghosh, D.K. / Schlichting, I. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Structures of nitric oxide synthase isoforms complexed with the inhibitor AR-R17477 suggest a rational basis for specificity and inhibitor design Authors: Fedorov, R. / Vasan, R. / Ghosh, D.K. / Schlichting, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vaf.cif.gz | 190.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vaf.ent.gz | 151.8 KB | Display | PDB format |
PDBx/mmJSON format | 1vaf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vaf_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 1vaf_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 1vaf_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 1vaf_validation.cif.gz | 54.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/1vaf ftp://data.pdbj.org/pub/pdb/validation_reports/va/1vaf | HTTPS FTP |
-Related structure data
Related structure data | 1vagC 1nodS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | The dimer in asymmetric unit is not a biological dimer, but the counterpart of the biological dimer for molecule having chain ID "A" can be obtained by application of the symmetry operation: (-y, -x, -z+5/6 ) and for molecule with chain ID "B": (-x, -x+y, -z+2/3 ). |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48498.168 Da / Num. of mol.: 2 Fragment: Inducible Nitric Oxide Synthase Oxygenase Domain (residues 77-495) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: NOS2, INOSL / Plasmid: PCWORI / Production host: Escherichia coli (E. coli) / References: UniProt: P29477, nitric-oxide synthase (NADPH) |
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-Non-polymers , 5 types, 189 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 3.93 Å3/Da / Density % sol: 68.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MES, SODIUM-MALONATE, EPPS, NACL, GLYCEROL, H4B, beta-MERCAPTOETHANOL, AR-R17477, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. all: 33741 / Num. obs: 33439 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rsym value: 0.058 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.9→3 Å / Mean I/σ(I) obs: 5.7 / Rsym value: 0.381 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1NOD Resolution: 2.9→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.9→8 Å
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