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Yorodumi- PDB-4uh5: Structure of human nNOS R354A G357D mutant heme domain in complex... -
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-Basic information
Entry | Database: PDB / ID: 4uh5 | ||||||
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Title | Structure of human nNOS R354A G357D mutant heme domain in complex with N1-(5-(2-(6-Amino-4-methylpyridin-2-yl)ethyl)pyridin-3-yl)-N1,N2- dimethylethane-1,2-diamine | ||||||
Components | NEURONAL NITRIC OXIDE SYNTHASE | ||||||
Keywords | OXIDOREDUCTASE / NITRIC OXIDE SYNTHASE | ||||||
Function / homology | Function and homology information positive regulation of membrane repolarization during ventricular cardiac muscle cell action potential / 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 / regulation of cardiac muscle contraction by calcium ion signaling / arginine binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel ...positive regulation of membrane repolarization during ventricular cardiac muscle cell action potential / 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 / regulation of cardiac muscle contraction by calcium ion signaling / arginine binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / 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 / regulation of cardiac muscle contraction / calcium channel regulator activity / regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase (NADPH) / sodium channel regulator activity / nitric oxide mediated signal transduction / nitric-oxide synthase activity / multicellular organismal response to stress / xenobiotic catabolic process / arginine catabolic process / striated muscle contraction / regulation of sodium ion transport / Ion homeostasis / nitric oxide biosynthetic process / negative regulation of blood pressure / photoreceptor inner segment / response to hormone / cell redox homeostasis / sarcoplasmic reticulum / cell periphery / vasodilation / sarcolemma / cellular response to growth factor stimulus / calcium-dependent protein binding / positive regulation of peptidyl-serine phosphorylation / FMN binding / NADP binding / flavin adenine dinucleotide binding / response to heat / scaffold protein binding / transmembrane transporter binding / response to lipopolysaccharide / dendritic spine / calmodulin binding / postsynaptic density / cytoskeleton / response to hypoxia / membrane raft / synapse / heme binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.983 Å | ||||||
Authors | Li, H. / Poulos, T.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: 2-Aminopyridines with a Truncated Side Chain to Improve Human Neuronal Nitric Oxide Synthase Inhibitory Potency and Selectivity. Authors: Kang, S. / Li, H. / Tang, W. / Martasek, P. / Roman, L.J. / 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 | 4uh5.cif.gz | 360.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uh5.ent.gz | 297.1 KB | Display | PDB format |
PDBx/mmJSON format | 4uh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uh5_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 4uh5_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 4uh5_validation.xml.gz | 34.9 KB | Display | |
Data in CIF | 4uh5_validation.cif.gz | 48.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/4uh5 ftp://data.pdbj.org/pub/pdb/validation_reports/uh/4uh5 | HTTPS FTP |
-Related structure data
Related structure data | 4ugzC 4uh0C 4uh1C 4uh2C 4uh3C 4uh4C 4uh6C 4uh7C 4uh8C 4uh9C 4uhaC 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: YES [R354A G357D] Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29475 |
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-Non-polymers , 6 types, 306 molecules
#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: 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: RMERGE 1.710 RPIM 1.555 CC ONE HALF 0.335 |
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Crystal grow | pH: 6.2 Details: 8-9% PED3350 40MM CITRIC ACID 60MM BISTRISPROPANE 10% GLYCEROL 5MM TCEP, pH 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.127 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 16, 2014 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. obs: 71749 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.4 / % possible all: 90.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.983→39.835 Å / SU ML: 0.35 / σ(F): 0.53 / Phase error: 31.63 / Stereochemistry target values: ML Details: RESIDUES 344 TO 348 IN CHAIN A AND 344 TO 353 IN CHAIN B ARE DISORDERED
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.983→39.835 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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