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Yorodumi- PDB-5uny: Structure of rat neuronal nitric oxide synthase heme domain in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uny | ||||||
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Title | Structure of rat neuronal nitric oxide synthase heme domain in complex with (RS)-3-[(2-amino-4-methylquinolin-7-yl)methoxy]-5-(2-(methylamino)propyl)benzonitrile | ||||||
Components | Nitric oxide synthase, brain | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / nitric / oxide / synthase / inhibitor / complex / heme / enzyme / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / retrograde trans-synaptic signaling by nitric oxide / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / positive regulation of sodium ion transmembrane transport ...Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / retrograde trans-synaptic signaling by nitric oxide / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / positive regulation of sodium ion transmembrane transport / response to nitric oxide / nitric oxide metabolic process / postsynaptic specialization, intracellular component / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / Ion homeostasis / negative regulation of cytosolic calcium ion concentration / peptidyl-cysteine S-nitrosylation / cadmium ion binding / positive regulation of the force of heart contraction / negative regulation of potassium ion transport / negative regulation of calcium ion transport / calyx of Held / behavioral response to cocaine / negative regulation of serotonin uptake / regulation of neurogenesis / nitric-oxide synthase (NADPH) / sodium channel regulator activity / response to vitamin E / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / negative regulation of insulin secretion / nitric oxide mediated signal transduction / nitric-oxide synthase activity / multicellular organismal response to stress / xenobiotic catabolic process / arginine catabolic process / NADPH binding / striated muscle contraction / regulation of sodium ion transport / nitric oxide-cGMP-mediated signaling / sarcoplasmic reticulum membrane / T-tubule / cellular response to epinephrine stimulus / : / nitric oxide biosynthetic process / negative regulation of blood pressure / photoreceptor inner segment / response to nutrient levels / potassium ion transport / response to hormone / sarcoplasmic reticulum / secretory granule / response to activity / positive regulation of long-term synaptic potentiation / establishment of localization in cell / cell periphery / female pregnancy / phosphoprotein binding / response to lead ion / response to nicotine / establishment of protein localization / cellular response to mechanical stimulus / vasodilation / response to organic cyclic compound / sarcolemma / cellular response to growth factor stimulus / response to peptide hormone / Z disc / response to estrogen / calcium-dependent protein binding / calcium ion transport / positive regulation of peptidyl-serine phosphorylation / FMN binding / ATPase binding / NADP binding / flavin adenine dinucleotide binding / nuclear membrane / response to heat / scaffold protein binding / response to ethanol / negative regulation of neuron apoptotic process / transmembrane transporter binding / mitochondrial outer membrane / response to lipopolysaccharide / dendritic spine / calmodulin binding / postsynaptic density / cytoskeleton / response to hypoxia / membrane raft / negative regulation of cell population proliferation / glutamatergic synapse / synapse / dendrite / heme binding / positive regulation of DNA-templated transcription / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / positive regulation of transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.82 Å | ||||||
Authors | Li, H. / Poulos, T.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Med. Chem. / Year: 2017 Title: Nitrile in the Hole: Discovery of a Small Auxiliary Pocket in Neuronal Nitric Oxide Synthase Leading to the Development of Potent and Selective 2-Aminoquinoline Inhibitors. Authors: Cinelli, M.A. / Li, H. / Chreifi, G. / 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 | 5uny.cif.gz | 369.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uny.ent.gz | 300.2 KB | Display | PDB format |
PDBx/mmJSON format | 5uny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uny_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 5uny_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 5uny_validation.xml.gz | 37.1 KB | Display | |
Data in CIF | 5uny_validation.cif.gz | 51.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/5uny ftp://data.pdbj.org/pub/pdb/validation_reports/un/5uny | HTTPS FTP |
-Related structure data
Related structure data | 5unrC 5unsC 5untC 5unuC 5unvC 5unwC 5unxC 5unzC 5uo0C 5uo1C 5uo2C 5uo3C 5uo4C 5uo5C 5uo6C 5uo7C 5uo8C 5uo9C 5uoaC 5uobC 5uocC 5uodC 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: 48812.527 Da / Num. of mol.: 2 / Fragment: UNP residues 297-718 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nos1, Bnos / Organ: brain / Plasmid: pCWori / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29476, nitric-oxide synthase (NADPH) |
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-Non-polymers , 7 types, 417 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #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: 2.48 Å3/Da / Density % sol: 50.4 % / Description: brick |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 20-24% PEG3350, 0.1 M MES, 0.14-0.20 M ammonium acetate, 10% ethylene glycol, 30 uM SDS, 5 mM GSH |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2016 / Details: graphite |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50 Å / Num. obs: 86968 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.82→1.87 Å / Redundancy: 5.5 % / Rmerge(I) obs: 5.301 / Mean I/σ(I) obs: 0.4 / Num. unique all: 4105 / CC1/2: 0.373 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Resolution: 1.82→39.226 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 34.07
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→39.226 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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