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Yorodumi- 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 | ||||||
Components | NITRIC OXIDE SYNTHASE, BRAIN | ||||||
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 / regulation of cardiac muscle contraction by calcium ion signaling / tetrahydrobiopterin binding / 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 / regulation of cardiac muscle contraction by calcium ion signaling / tetrahydrobiopterin binding / 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 / regulation of cardiac muscle contraction / calcium channel regulator activity / negative regulation of serotonin uptake / nitric-oxide synthase (NADPH) / regulation of ryanodine-sensitive calcium-release channel activity / sodium channel regulator activity / nitric oxide mediated signal transduction / nitric-oxide synthase activity / xenobiotic catabolic process / multicellular organismal response to stress / arginine catabolic process / striated muscle contraction / Ion homeostasis / regulation of sodium ion transport / nitric oxide biosynthetic process / negative regulation of blood pressure / photoreceptor inner segment / response to hormone / cell redox homeostasis / sarcoplasmic reticulum / 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 / response to hypoxia / calmodulin binding / membrane raft / heme binding / synapse / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Li, H. / Poulos, T.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v3u.cif.gz | 706.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v3u.ent.gz | 583.5 KB | Display | PDB format |
PDBx/mmJSON format | 4v3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v3u_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 4v3u_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 4v3u_validation.xml.gz | 71.6 KB | Display | |
Data in CIF | 4v3u_validation.cif.gz | 99.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/4v3u ftp://data.pdbj.org/pub/pdb/validation_reports/v3/4v3u | 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 (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) 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, 921 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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