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Yorodumi- PDB-3nm0: Structure of rat neuronal nitric oxide synthase heme domain in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nm0 | ||||||
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Title | Structure of rat neuronal nitric oxide synthase heme domain in complex with 6-(((3R,4R)-4-(2-(2,2-Difluoro-2-phenylethylamino)ethoxy) pyrrolidin-3-yl)methyl)-4-methyl-3,4,5,6-tetrahydropyridin-2-amine | ||||||
Components | Nitric oxide synthase, brain | ||||||
Keywords | OXIDOREDUCTASE / nitric oxide synthase / heme thiolate enzyme inhibitor | ||||||
Function / homology | Function and homology information positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / retrograde trans-synaptic signaling by nitric oxide / Ion homeostasis ...positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / azurophil granule / negative regulation of vasoconstriction / retrograde trans-synaptic signaling by nitric oxide / Ion homeostasis / positive regulation of sodium ion transmembrane transport / response to nitric oxide / postsynaptic specialization, intracellular component / negative regulation of cytosolic calcium ion concentration / peptidyl-cysteine S-nitrosylation / behavioral response to cocaine / postsynaptic density, intracellular component / cadmium ion binding / positive regulation of the force of heart contraction / negative regulation of potassium ion transport / calyx of Held / negative regulation of calcium ion transport / negative regulation of serotonin uptake / sodium channel regulator activity / regulation of neurogenesis / striated muscle contraction / regulation of postsynaptic membrane potential / negative regulation of insulin secretion / response to vitamin E / nitric-oxide synthase (NADPH) / multicellular organismal response to stress / xenobiotic catabolic process / nitric-oxide synthase activity / negative regulation of peptidyl-serine phosphorylation / nitric oxide mediated signal transduction / arginine catabolic process / NADPH binding / regulation of sodium ion transport / response to organonitrogen compound / sarcoplasmic reticulum membrane / cellular response to epinephrine stimulus / T-tubule / photoreceptor inner segment / nitric oxide biosynthetic process / negative regulation of blood pressure / response to hormone / response to nutrient levels / response to activity / response to nicotine / sarcoplasmic reticulum / muscle contraction / secretory granule / female pregnancy / positive regulation of long-term synaptic potentiation / cell periphery / establishment of localization in cell / phosphoprotein binding / response to lead ion / sarcolemma / establishment of protein localization / potassium ion transport / response to organic cyclic compound / response to peptide hormone / cellular response to growth factor stimulus / Z disc / vasodilation / cellular response to mechanical stimulus / response to estrogen / calcium-dependent protein binding / calcium ion transport / FMN binding / flavin adenine dinucleotide binding / positive regulation of peptidyl-serine phosphorylation / NADP binding / ATPase binding / response to heat / scaffold protein binding / response to ethanol / nuclear membrane / negative regulation of neuron apoptotic process / mitochondrial outer membrane / transmembrane transporter binding / response to lipopolysaccharide / dendritic spine / postsynaptic density / response to hypoxia / cytoskeleton / calmodulin binding / membrane raft / negative regulation of cell population proliferation / dendrite / glutamatergic synapse / synapse / heme binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.81 Å | ||||||
Authors | Li, H. / Delker, S.L. / Poulos, T.L. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Potent, highly selective, and orally bioavailable gem-difluorinated monocationic inhibitors of neuronal nitric oxide synthase. Authors: Xue, F. / Li, H. / Delker, S.L. / Fang, J. / Martasek, P. / Roman, L.J. / 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 | 3nm0.cif.gz | 366.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nm0.ent.gz | 296.3 KB | Display | PDB format |
PDBx/mmJSON format | 3nm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/3nm0 ftp://data.pdbj.org/pub/pdb/validation_reports/nm/3nm0 | HTTPS FTP |
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-Related structure data
Related structure data | 3nltC 3nluC 3nlvC 3nlwC 3nlxC 3nlyC 3nlzC 1om4S 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: 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 / Plasmid: pCWori / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29476, nitric-oxide synthase (NADPH) |
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-Non-polymers , 6 types, 468 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ZN / | #7: 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: 2.43 Å3/Da / Density % sol: 49.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: PEG 3350, MES, ammonium acetate SDS, GSH, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 30, 2009 / 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: 1.81→50 Å / Num. obs: 86908 / % possible obs: 99 % / Redundancy: 4 % / Biso Wilson estimate: 26.49 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.81→1.84 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.38 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1OM4 Resolution: 1.81→38.11 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.083 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.115 / 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: 36.871 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→38.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.856 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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