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Yorodumi- PDB-1p6k: Rat neuronal NOS D597N mutant heme domain with L-N(omega)-nitroar... -
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-Basic information
Entry | Database: PDB / ID: 1p6k | ||||||
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Title | Rat neuronal NOS D597N mutant heme domain with L-N(omega)-nitroarginine-2,4-L-diaminobutyric amide bound | ||||||
Components | Nitric-oxide synthase, brainNitric oxide synthase | ||||||
Keywords | OXIDOREDUCTASE / nitric oxide synthase / heme-enzyme | ||||||
Function / homology | Function and homology information 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 / positive regulation of sodium ion transmembrane transport / response to nitric oxide ...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 / positive regulation of sodium ion transmembrane transport / response to nitric oxide / Ion homeostasis / nitric oxide metabolic process / postsynaptic specialization, intracellular component / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of cytosolic calcium ion concentration / peptidyl-cysteine S-nitrosylation / cadmium ion binding / behavioral response to cocaine / 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 / regulation of neurogenesis / sodium channel regulator activity / negative regulation of insulin secretion / response to vitamin E / nitric-oxide synthase (NADPH) / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / multicellular organismal response to stress / nitric-oxide synthase activity / xenobiotic catabolic process / negative regulation of peptidyl-serine phosphorylation / NADPH binding / striated muscle contraction / arginine catabolic process / regulation of sodium ion transport / nitric oxide mediated signal transduction / T-tubule / sarcoplasmic reticulum membrane / response to organonitrogen compound / cellular response to epinephrine stimulus / nitric oxide biosynthetic process / negative regulation of blood pressure / photoreceptor inner segment / response to nutrient levels / response to activity / sarcoplasmic reticulum / secretory granule / response to hormone / positive regulation of long-term synaptic potentiation / female pregnancy / muscle contraction / establishment of localization in cell / cell periphery / phosphoprotein binding / response to lead ion / response to nicotine / establishment of protein localization / potassium ion transport / response to organic cyclic compound / sarcolemma / cellular response to growth factor stimulus / response to peptide hormone / Z disc / cellular response to mechanical stimulus / response to estrogen / vasodilation / calcium ion transport / calcium-dependent protein binding / FMN binding / positive regulation of peptidyl-serine phosphorylation / NADP binding / flavin adenine dinucleotide binding / ATPase binding / response to heat / scaffold protein binding / nuclear membrane / response to ethanol / mitochondrial outer membrane / negative regulation of neuron apoptotic process / transmembrane transporter binding / response to lipopolysaccharide / dendritic spine / postsynaptic density / cytoskeleton / calmodulin binding / response to hypoxia / membrane raft / negative regulation of cell population proliferation / glutamatergic synapse / synapse / dendrite / 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 Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.78 Å | ||||||
Authors | Flinspach, M.L. / Li, H. / Jamal, J. / Yang, W. / Huang, H. / Hah, J.-M. / Gomez-Vidal, J.A. / Litzinger, E.A. / Silverman, R.B. / Poulos, T.L. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Structural basis for dipeptide amide isoform-selective inhibition of neuronal nitric oxide synthase. Authors: Flinspach, M.L. / Li, H. / Jamal, J. / Yang, W. / Huang, H. / Hah, J.M. / Gomez-Vidal, J.A. / Litzinger, E.A. / Silverman, R.B. / Poulos, T.L. #1: Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: CRYSTAL STRUCTURE OF CONSTITUTIVE ENDOTHELIAL NITRIC OXIDE SYNTHASE: A PARADIGM FOR PTERIN FUNCTION INVOLVING A NOVEL METAL CENTER Authors: Raman, C.S. / Li, H. / Martasek, P. / Kral, V. / Masters, B.S.S. / Poulos, T.L. #2: Journal: Biochemistry / Year: 2002 Title: The novel binding mode of N-alkyl-N'-hydroxyguanidine to neuronal nitric oxide synthase provides mechanistic insights into NO biosynthesis Authors: Li, H. / Shimizu, H. / Flinspach, M. / Jamal, J. / Yang, W. / Xian, M. / Cai, T. / Wen, E.Z. / Jia, Q. / Wang, P.G. / Poulos, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p6k.cif.gz | 198.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p6k.ent.gz | 154.5 KB | Display | PDB format |
PDBx/mmJSON format | 1p6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/1p6k ftp://data.pdbj.org/pub/pdb/validation_reports/p6/1p6k | HTTPS FTP |
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-Related structure data
Related structure data | 1p6hC 1p6iC 1p6jC 1p6lC 1p6mC 1p6nC 1q2oC 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: 48754.492 Da / Num. of mol.: 2 / Mutation: D597N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pCWori / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29476, nitric-oxide synthase (NADPH) |
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-Non-polymers , 7 types, 584 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Chemical | #6: Chemical | #7: Chemical | #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: 2.39 Å3/Da / Density % sol: 48.61 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: PEG4000, MES, ammonium acetate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 280K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 5 ℃ / Method: vapor diffusion, sitting drop / Details: Li, H., (2002) Biochemistry, 41, 13868. / PH range low: 6 / PH range high: 5.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL11-1 / Wavelength: 1.033 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2003 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. obs: 91867 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.524 |
Reflection | *PLUS % possible obs: 99.3 % / Num. measured all: 444168 |
Reflection shell | *PLUS % possible obs: 97.7 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.78→49.38 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.0371 Å2 / ksol: 0.369971 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.78→49.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.84 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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