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Yorodumi- PDB-4uh0: Structure of rat neuronal nitric oxide synthase heme domain in co... -
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-Basic information
Entry | Database: PDB / ID: 4uh0 | ||||||
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Title | Structure of rat neuronal nitric oxide synthase heme domain in complex with N1-(6-(2-(6-Amino-4-methylpyridin-2-yl)ethyl)pyridin-2- yl)-N1,N2-dimethylethane-1,2-diamine | ||||||
Components | NITRIC OXIDE SYNTHASE, BRAIN | ||||||
Keywords | OXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / INHIBITOR COMPLEX | ||||||
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 / OTHER / Resolution: 2.039 Å | ||||||
Authors | Li, H. / Poulos, T.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: 2-Aminopyridines with a Truncated Side Chain to Improve Human Neuronal Nitric Oxide Synthase Inhibitory Potency and Selectivity. Authors: Kang, S. / Li, H. / Tang, W. / 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 | 4uh0.cif.gz | 353.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uh0.ent.gz | 299.5 KB | Display | PDB format |
PDBx/mmJSON format | 4uh0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/4uh0 ftp://data.pdbj.org/pub/pdb/validation_reports/uh/4uh0 | HTTPS FTP |
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-Related structure data
Related structure data | 4ugzC 4uh1C 4uh2C 4uh3C 4uh4C 4uh5C 4uh6C 4uh7C 4uh8C 4uh9C 4uhaC 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: HEME DOMAIN, UNP RESIDUES 297-718 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / 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, 386 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: 2.46 Å3/Da / Density % sol: 50.1 % / Description: RPIM 0.456 CC ONE HALF 0.933 |
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Crystal grow | pH: 5.8 Details: 20-22% PEG3350 0.1M MES, PH5.8 140-200 MM AMMONIUM ACETATE 10% ETHYLENE GLYCOL 5 MM GSH 30UM SDS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 16, 2012 / 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: 2.03→50 Å / Num. obs: 61372 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 37.07 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 2.03→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.039→49.787 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 27.12 / Stereochemistry target values: ML Details: RESIDUES 339 TO 349 IN CHAIN A AND 339 TO 347 IN CHAIN B ARE DISORDERED.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.039→49.787 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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