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Yorodumi- PDB-1m9m: human endothelial nitric oxide synthase with 6-nitroindazole bound -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m9m | ||||||
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Title | human endothelial nitric oxide synthase with 6-nitroindazole bound | ||||||
Components | endothelial Nitric-oxide synthase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / NOSTRIN mediated eNOS trafficking / negative regulation of muscle hyperplasia / regulation of nervous system process / smooth muscle hyperplasia / response to fluid shear stress / ovulation from ovarian follicle / pulmonary valve morphogenesis / negative regulation of biomineral tissue development ...regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / NOSTRIN mediated eNOS trafficking / negative regulation of muscle hyperplasia / regulation of nervous system process / smooth muscle hyperplasia / response to fluid shear stress / ovulation from ovarian follicle / pulmonary valve morphogenesis / negative regulation of biomineral tissue development / positive regulation of guanylate cyclase activity / Nitric oxide stimulates guanylate cyclase / regulation of systemic arterial blood pressure by endothelin / ROS and RNS production in phagocytes / tetrahydrobiopterin binding / aortic valve morphogenesis / arginine binding / endocardial cushion morphogenesis / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / cadmium ion binding / negative regulation of potassium ion transport / negative regulation of calcium ion transport / actin monomer binding / negative regulation of platelet activation / endothelial cell migration / nitric-oxide synthase (NADPH) / positive regulation of blood vessel endothelial cell migration / blood vessel remodeling / nitric oxide mediated signal transduction / nitric-oxide synthase activity / eNOS activation / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of sodium ion transport / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / lipopolysaccharide-mediated signaling pathway / homeostasis of number of cells within a tissue / nitric oxide biosynthetic process / negative regulation of blood pressure / removal of superoxide radicals / blood vessel diameter maintenance / potassium ion transport / negative regulation of smooth muscle cell proliferation / lung development / VEGFR2 mediated vascular permeability / response to hormone / cell redox homeostasis / mitochondrion organization / caveola / establishment of localization in cell / regulation of blood pressure / vasodilation / positive regulation of angiogenesis / calcium ion transport / endocytic vesicle membrane / FMN binding / NADP binding / flavin adenine dinucleotide binding / response to heat / scaffold protein binding / angiogenesis / in utero embryonic development / Extra-nuclear estrogen signaling / response to lipopolysaccharide / calmodulin binding / cytoskeleton / Golgi membrane / negative regulation of cell population proliferation / heme binding / positive regulation of gene expression / Golgi apparatus / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Rosenfeld, R.J. / Garcin, E.D. / Panda, K. / Andersson, G. / Aberg, A. / Wallace, A.V. / Stuehr, D.J. / Tainer, J.A. / Getzoff, E.D. | ||||||
Citation | Journal: Biochemistry / Year: 2002 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: Journal: Science / Year: 1998 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m9m.cif.gz | 184 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m9m.ent.gz | 143.7 KB | Display | PDB format |
PDBx/mmJSON format | 1m9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m9m_validation.pdf.gz | 577.3 KB | Display | wwPDB validaton report |
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Full document | 1m9m_full_validation.pdf.gz | 585.7 KB | Display | |
Data in XML | 1m9m_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 1m9m_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/1m9m ftp://data.pdbj.org/pub/pdb/validation_reports/m9/1m9m | HTTPS FTP |
-Related structure data
Related structure data | 1m8dC 1m8eC 1m8hC 1m8iC 1m9jC 1m9kC 1m9qC 1m9rC 1m9tC 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: 46920.156 Da / Num. of mol.: 2 / Fragment: oxygenase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P29474, nitric-oxide synthase (NADPH) |
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-Non-polymers , 7 types, 425 molecules
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | ChemComp-NA / | ||||||||
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: 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: 2.62 Å3/Da / Density % sol: 53.1 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: NaCl, MPD, PEG, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / 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: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 29, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. all: 69487 / Num. obs: 69487 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.96→2.01 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.7 / Num. unique all: 4142 / Rsym value: 0.321 / % possible all: 87.2 |
Reflection | *PLUS Num. measured all: 290276 |
Reflection shell | *PLUS % possible obs: 87.2 % / Num. unique obs: 4142 / Num. measured obs: 8898 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→45.03 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: 23.1837 Å2 / ksol: 0.307494 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.2 Å2
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Refine analyze | Luzzati coordinate error free: 0.27 Å / Luzzati sigma a free: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→45.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.08 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / Rfactor Rwork: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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