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- PDB-3jt8: Structure of neuronal nitric oxide synthase heme domain complexed... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3jt8 | ||||||
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Title | Structure of neuronal nitric oxide synthase heme domain complexed with N~5~-{3-[(1-methylethyl)sulfanyl]propanimidoyl}-L-ornithine | ||||||
![]() | Nitric oxide synthase, brain | ||||||
![]() | OXIDOREDUCTASE / nitric oxide synthase / heme-thiolate enzyme / substrate-analogue inhibitor / thioether heme ligand / Alternative splicing / Calmodulin-binding / Cell membrane / Cell projection / FAD / FMN / Heme / Iron / Membrane / Metal-binding / NADP | ||||||
Function / homology | ![]() Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / 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 ...Nitric oxide stimulates guanylate cyclase / negative regulation of hepatic stellate cell contraction / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / 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 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 / calyx of Held / negative regulation of potassium ion transport / behavioral response to cocaine / negative regulation of calcium ion transport / negative regulation of serotonin uptake / regulation of neurogenesis / response to vitamin E / nitric-oxide synthase (NADPH) / sodium channel regulator activity / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / negative regulation of insulin secretion / nitric oxide mediated signal transduction / multicellular organismal response to stress / nitric-oxide synthase activity / xenobiotic catabolic process / NADPH binding / arginine catabolic process / striated muscle contraction / regulation of sodium ion transport / nitric oxide-cGMP-mediated signaling / T-tubule / response to organonitrogen compound / sarcoplasmic reticulum membrane / cellular response to epinephrine stimulus / nitric oxide biosynthetic process / negative regulation of blood pressure / photoreceptor inner segment / response to nutrient levels / response to hormone / response to activity / secretory granule / sarcoplasmic reticulum / positive regulation of long-term synaptic potentiation / establishment of localization in cell / muscle contraction / cell periphery / female pregnancy / phosphoprotein binding / response to lead ion / response to nicotine / potassium ion transport / establishment of protein localization / 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 / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, H. / Poulos, T.L. | ||||||
![]() | ![]() Title: Heme-coordinating inhibitors of neuronal nitric oxide synthase. Iron-thioether coordination is stabilized by hydrophobic contacts without increased inhibitor potency. Authors: Martell, J.D. / Li, H. / Doukov, T. / Martasek, P. / Roman, L.J. / Soltis, M. / Poulos, T.L. / Silverman, R.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 312.5 KB | Display | ![]() |
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PDB format | ![]() | 245.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 37.5 KB | Display | |
Data in CIF | ![]() | 52.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jt3C ![]() 3jt4C ![]() 3jt5C ![]() 3jt6C ![]() 3jt7C ![]() 3jt9C ![]() 3jtaC ![]() 1om4S 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48812.527 Da / Num. of mol.: 2 / Fragment: UNP residues 297-718 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 390 molecules ![](data/chem/img/HEM.gif)
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#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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.82 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: PEG3350, MES, ammonium acetate, SDS, GSH, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2008 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 70347 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 30.21 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.45 / % possible all: 94.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1OM4 Resolution: 1.95→38.11 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 10.02 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.145 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.796 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→38.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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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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