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Yorodumi- PDB-1qwc: Rat neuronal nitric oxide synthase oxygenase domain in complex wi... -
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-Basic information
Entry | Database: PDB / ID: 1qwc | ||||||
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Title | Rat neuronal nitric oxide synthase oxygenase domain in complex with W1400 inhibitor. | ||||||
Components | Nitric-oxide synthase, brain | ||||||
Keywords | OXIDOREDUCTASE / Rat nNOSoxy W1400 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Fedorov, R. / Hartmann, E. / Ghosh, D.K. / Schlichting, I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Structural basis for the specificity of the nitric-oxide synthase inhibitors W1400 and Nomega-propyl-L-Arg for the inducible and neuronal isoforms. Authors: Fedorov, R. / Hartmann, E. / 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 | 1qwc.cif.gz | 107.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qwc.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 1qwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qwc_validation.pdf.gz | 855.1 KB | Display | wwPDB validaton report |
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Full document | 1qwc_full_validation.pdf.gz | 872.8 KB | Display | |
Data in XML | 1qwc_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 1qwc_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/1qwc ftp://data.pdbj.org/pub/pdb/validation_reports/qw/1qwc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48580.203 Da / Num. of mol.: 1 / Fragment: residues 298-716 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: NOS1 OR BNOS / Plasmid: pCWori / Production host: Escherichia coli (E. coli) / References: UniProt: P29476, nitric-oxide synthase (NADPH) |
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-Non-polymers , 5 types, 210 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-H4B / |
#5: Chemical | ChemComp-14W / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.26 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: HEPES, DTT, PEG3350, EPPS, NaCl, glycerol, H4B, β-mercaptoethanol, W1400., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 8, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 17897 / Num. obs: 17658 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 31.2 Å2 / Rsym value: 0.093 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.3→2.4 Å / Mean I/σ(I) obs: 5.1 / Rsym value: 0.373 / % possible all: 93.1 |
Reflection | *PLUS Num. measured all: 125740 / Rmerge(I) obs: 0.093 |
Reflection shell | *PLUS % possible obs: 93.1 % / Rmerge(I) obs: 0.373 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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