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Open data
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Basic information
Entry | Database: PDB / ID: 1m8d | ||||||
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Title | inducible nitric oxide synthase with Chlorzoxazone bound | ||||||
![]() | Inducible Nitric Oxide Synthase | ||||||
![]() | OXIDOREDUCTASE / inhibitor-induced conformational change | ||||||
Function / homology | ![]() Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / Peroxisomal protein import / cAMP-dependent protein kinase regulator activity / prostaglandin secretion / positive regulation of killing of cells of another organism / tetrahydrobiopterin binding / arginine binding / cortical cytoskeleton ...Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / Peroxisomal protein import / cAMP-dependent protein kinase regulator activity / prostaglandin secretion / positive regulation of killing of cells of another organism / tetrahydrobiopterin binding / arginine binding / cortical cytoskeleton / superoxide metabolic process / cGMP-mediated signaling / nitric-oxide synthase binding / regulation of cytokine production involved in inflammatory response / peptidyl-cysteine S-nitrosylation / cellular response to cytokine stimulus / regulation of insulin secretion / cellular response to organic cyclic compound / nitric-oxide synthase (NADPH) / blood vessel remodeling / nitric oxide mediated signal transduction / response to tumor necrosis factor / nitric-oxide synthase activity / arginine catabolic process / nitric oxide biosynthetic process / negative regulation of blood pressure / response to hormone / positive regulation of interleukin-8 production / response to bacterium / Hsp90 protein binding / negative regulation of protein catabolic process / beta-catenin binding / regulation of blood pressure / cellular response to type II interferon / circadian rhythm / peroxisome / positive regulation of interleukin-6 production / cellular response to xenobiotic stimulus / FMN binding / NADP binding / actin binding / regulation of cell population proliferation / flavin adenine dinucleotide binding / cellular response to lipopolysaccharide / response to lipopolysaccharide / calmodulin binding / response to hypoxia / intracellular signal transduction / defense response to bacterium / cadherin binding / inflammatory response / positive regulation of apoptotic process / negative regulation of gene expression / heme binding / protein kinase binding / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rosenfeld, R.J. / Garcin, E.D. / Panda, K. / Andersson, G. / Aberg, A. / Wallace, A.V. / Stuehr, D.J. / Tainer, J.A. / Getzoff, E.D. | ||||||
![]() | ![]() Title: Conformational Changes in Nitric Oxide Synthases Induced by Chlorzoxazone and Nitroindazoles: Crystallographic and Computational Analyses of Inhibitor Potency Authors: Rosenfeld, R.J. / Garcin, E.D. / Panda, K. / Andersson, G. / Aberg, A. / Wallace, A.V. / Morris, G.M. / Olson, A.J. / Stuehr, D.J. / Tainer, J.A. / Getzoff, E.D. #1: ![]() Title: Structure of nitric oxide synthase oxygenase dimer with pterin and substrate Authors: Crane, B.R. / Arvai, A.S. / Ghosh, D.K. / Wu, C. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195 KB | Display | ![]() |
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PDB format | ![]() | 152.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 624.9 KB | Display | ![]() |
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Full document | ![]() | 639.1 KB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 31.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1m8eC ![]() 1m8hC ![]() 1m8iC ![]() 1m9jC ![]() 1m9kC ![]() 1m9mC ![]() 1m9qC ![]() 1m9rC ![]() 1m9tC ![]() 1df1S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological active assembly is a dimer. There are two monomers in the asymmetric unit, each monomer generates an active dimer. To get one dimer, apply the following symmetry operation to chain A: 1+y-x, y, 1/2-z. / To get a second dimer, apply the following symmetry operation to chain B: 2-x, 1-x+y, 2/3-z+5/3 |
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Components
-Protein / Sugars , 2 types, 3 molecules AB![](data/chem/img/BOG.gif)
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#1: Protein | Mass: 50208.027 Da / Num. of mol.: 2 / Fragment: Oxygenase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #6: Sugar | ChemComp-BOG / | |
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-Non-polymers , 6 types, 341 molecules ![](data/chem/img/SO4.gif)
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#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #7: Chemical | ChemComp-EDO / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.59 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Lithium Sulfate, B-octyl-glucodise, MES buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.6 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 12, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→20 Å / Num. obs: 61961 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.96 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5149 / Rsym value: 0.366 / % possible all: 80.8 |
Reflection | *PLUS Num. measured all: 306715 |
Reflection shell | *PLUS % possible obs: 80.8 % / Num. unique obs: 5149 / Num. measured obs: 13672 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1DF1 Resolution: 2.35→19.84 Å / Rfactor Rfree error: 0.005 / 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: 30.321 Å2 / ksol: 0.303507 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.3 Å2
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Refine analyze | Luzzati coordinate error free: 0.39 Å / Luzzati sigma a free: 0.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→19.84 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.245 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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