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Yorodumi- PDB-6po8: Structure of human neuronal nitric oxide synthase R354A/G357D mut... -
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-Basic information
Entry | Database: PDB / ID: 6po8 | ||||||
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Title | Structure of human neuronal nitric oxide synthase R354A/G357D mutant heme domain in complex with 4-((4-(2-Amino-4-methylquinolin-7-yl)-2-(aminomethyl)phenoxy)methyl)benzonitrile | ||||||
Components | Nitric oxide synthase, brain | ||||||
Keywords | oxidoreductase/oxidoreductase inhibitor / nitric oxide synthase inhibitor complex heme enzyme / OXIDOREDUCTASE / oxidoreductase-oxidoreductase inhibitor complex | ||||||
Function / homology | Function and homology information negative regulation of calcium ion transport into cytosol / Nitric oxide stimulates guanylate cyclase / myoblast fusion / ROS and RNS production in phagocytes / negative regulation of hydrolase activity / tetrahydrobiopterin binding / arginine binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / retrograde trans-synaptic signaling by nitric oxide / positive regulation of sodium ion transmembrane transport ...negative regulation of calcium ion transport into cytosol / Nitric oxide stimulates guanylate cyclase / myoblast fusion / ROS and RNS production in phagocytes / negative regulation of hydrolase activity / tetrahydrobiopterin binding / arginine binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / retrograde trans-synaptic signaling by nitric oxide / positive regulation of sodium ion transmembrane transport / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 / negative regulation of serotonin uptake / sodium channel regulator activity / striated muscle contraction / nitric-oxide synthase (NADPH) / regulation of cardiac muscle contraction / multicellular organismal response to stress / nitric-oxide synthase activity / xenobiotic catabolic process / arginine catabolic process / regulation of sodium ion transport / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / nitric oxide mediated signal transduction / nitric oxide biosynthetic process / negative regulation of blood pressure / photoreceptor inner segment / response to hormone / cell redox homeostasis / sarcoplasmic reticulum / muscle contraction / cell periphery / sarcolemma / cellular response to growth factor stimulus / vasodilation / calcium-dependent protein binding / FMN binding / flavin adenine dinucleotide binding / positive regulation of peptidyl-serine phosphorylation / NADP binding / response to heat / scaffold protein binding / transmembrane transporter binding / response to lipopolysaccharide / dendritic spine / postsynaptic density / response to hypoxia / cytoskeleton / calmodulin binding / membrane raft / synapse / heme binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.898 Å | ||||||
Authors | Li, H. / Poulos, T.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: First Contact: 7-Phenyl-2-Aminoquinolines, Potent and Selective Neuronal Nitric Oxide Synthase Inhibitors That Target an Isoform-Specific Aspartate. Authors: Cinelli, M.A. / Reidl, C.T. / Li, H. / Chreifi, G. / Poulos, T.L. / Silverman, R.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6po8.cif.gz | 371.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6po8.ent.gz | 301.5 KB | Display | PDB format |
PDBx/mmJSON format | 6po8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/6po8 ftp://data.pdbj.org/pub/pdb/validation_reports/po/6po8 | HTTPS FTP |
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-Related structure data
Related structure data | 6pmvC 6pmwC 6pmxC 6pmyC 6pmzC 6pn0C 6pn1C 6pn2C 6pn3C 6pn4C 6pn5C 6pn6C 6pn7C 6pn8C 6pn9C 6pnaC 6pnbC 6pncC 6pndC 6pneC 6pnfC 6pngC 6pnhC 6po5C 6po7C 6po9C 6poaC 6pobC 6pocC 6potC 6pouC 6povC 6powC 6poxC 6poyC 6pozC 6pp0C 6pp1C 6pp2C 6pp3C 6pp4C 4uh5S S: Starting model for refinement 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: 48784.496 Da / Num. of mol.: 2 / Mutation: R354A,G357D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NOS1 / Organ: brain / Plasmid: pCWori / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29475, nitric-oxide synthase (NADPH) |
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-Non-polymers , 5 types, 752 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ZN / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.74 Å3/Da / Density % sol: 55.2 % / Description: plates |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 8% PEG3350 35mM citric acid 65mM Bis-Tris-Propane 10% glycerol 5mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2017 / Details: mirrors |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.898→60 Å / Num. obs: 83692 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.047 / Rsym value: 0.155 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.947 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4485 / CC1/2: 0.605 / Rpim(I) all: 0.603 / Rsym value: 1.947 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4UH5 Resolution: 1.898→38.492 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 25.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.898→38.492 Å
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Refine LS restraints |
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LS refinement shell |
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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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