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- PDB-4v3u: Structure of human nNOS R354A G357D mutant heme domain in complex... -
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Basic information
Entry | Database: PDB / ID: 4v3u | ||||||
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Title | Structure of human nNOS R354A G357D mutant heme domain in complex with N-2-(2-(1H-imidazol-1-yl)pyrimidin-4-yl)ethyl-3-(pyridin-3-yl) propan-1-amine | ||||||
![]() | NITRIC OXIDE SYNTHASE, BRAIN | ||||||
![]() | OXIDOREDUCTASE / NITRIC OXIDE SYNTHASE | ||||||
Function / homology | ![]() 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 / 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 / calcium channel regulator activity / regulation of cardiac muscle contraction / nitric-oxide synthase (NADPH) / sodium channel regulator activity / nitric oxide mediated signal transduction / multicellular organismal response to stress / nitric-oxide synthase activity / xenobiotic catabolic process / arginine catabolic process / striated muscle contraction / regulation of sodium ion transport / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / 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 / positive regulation of peptidyl-serine phosphorylation / NADP binding / flavin adenine dinucleotide binding / response to heat / scaffold protein binding / transmembrane transporter binding / response to lipopolysaccharide / dendritic spine / postsynaptic density / cytoskeleton / calmodulin binding / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, H. / Poulos, T.L. | ||||||
![]() | ![]() Title: Novel 2,4-Disubstituted Pyrimidines as Potent, Selective, and Cell-Permeable Inhibitors of Neuronal Nitric Oxide Synthase. Authors: Mukherjee, P. / Li, H. / Sevrioukova, I. / Chreifi, G. / Martasek, P. / Roman, L.J. / 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 | ![]() | 706.4 KB | Display | ![]() |
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PDB format | ![]() | 583.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 71.6 KB | Display | |
Data in CIF | ![]() | 99.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d2yC ![]() 4d2zC ![]() 4d30C ![]() 4d31C ![]() 4d32C ![]() 4d33C ![]() 4d34C ![]() 4d35C ![]() 4d36C ![]() 4d37C ![]() 4d38C ![]() 4d39C ![]() 4d3aC ![]() 4d3bC ![]() 4uchC ![]() 4v3vC ![]() 4v3wC ![]() 4v3xC ![]() 4v3yC ![]() 4v3zC ![]() 4d1nS 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, 4 molecules ABCD
#1: Protein | Mass: 48655.316 Da / Num. of mol.: 4 / Fragment: RESIDUES 302-721 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 921 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/H4B.gif)
![](data/chem/img/EG8.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/H4B.gif)
![](data/chem/img/EG8.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-H4B / #4: Chemical | ChemComp-EG8 / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.8 % / Description: RPIM 1.390 CC ONE HALF 0.245 |
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Crystal grow | pH: 6.2 Details: 11-13% PEG3350, 40MM CITRIC ACID 60MM BIS-TRIS-PROPANE, 10% GLYCEROL, 5 MM TCEP, pH 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2014 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 108522 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 31.04 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 0.7 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4D1N Resolution: 2.3→78.798 Å / SU ML: 0.36 / σ(F): 0.01 / Phase error: 26.69 / Stereochemistry target values: ML Details: RESIDUES 344 TO 352 IN BOTH CHAINS B AND D 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: 2.3→78.798 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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