[English] 日本語
Yorodumi- PDB-6pp3: Structure of human endothelial nitric oxide synthase heme domain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pp3 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of human endothelial nitric oxide synthase heme domain in complex with 7-(3-(Aminomethyl)-4-(pyridin-2-ylmethoxy)phenyl)-4-methylquinolin-2-amine | ||||||
Components | Nitric oxide synthase, endothelial | ||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / nitric oxide synthase inhibitor complex heme enzyme / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / NOSTRIN mediated eNOS trafficking / negative regulation of muscle hyperplasia / regulation of nervous system process / smooth muscle hyperplasia / response to fluid shear stress / ovulation from ovarian follicle / pulmonary valve morphogenesis / negative regulation of biomineral tissue development ...regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / NOSTRIN mediated eNOS trafficking / negative regulation of muscle hyperplasia / regulation of nervous system process / smooth muscle hyperplasia / response to fluid shear stress / ovulation from ovarian follicle / pulmonary valve morphogenesis / negative regulation of biomineral tissue development / positive regulation of guanylate cyclase activity / Nitric oxide stimulates guanylate cyclase / regulation of systemic arterial blood pressure by endothelin / ROS and RNS production in phagocytes / tetrahydrobiopterin binding / aortic valve morphogenesis / arginine binding / endocardial cushion morphogenesis / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / cadmium ion binding / negative regulation of potassium ion transport / negative regulation of calcium ion transport / actin monomer binding / negative regulation of platelet activation / endothelial cell migration / nitric-oxide synthase (NADPH) / positive regulation of blood vessel endothelial cell migration / blood vessel remodeling / nitric oxide mediated signal transduction / nitric-oxide synthase activity / eNOS activation / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of sodium ion transport / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / lipopolysaccharide-mediated signaling pathway / homeostasis of number of cells within a tissue / nitric oxide biosynthetic process / negative regulation of blood pressure / removal of superoxide radicals / blood vessel diameter maintenance / potassium ion transport / negative regulation of smooth muscle cell proliferation / lung development / VEGFR2 mediated vascular permeability / response to hormone / cell redox homeostasis / mitochondrion organization / caveola / establishment of localization in cell / regulation of blood pressure / vasodilation / positive regulation of angiogenesis / calcium ion transport / endocytic vesicle membrane / FMN binding / NADP binding / flavin adenine dinucleotide binding / response to heat / scaffold protein binding / angiogenesis / in utero embryonic development / Extra-nuclear estrogen signaling / response to lipopolysaccharide / calmodulin binding / cytoskeleton / Golgi membrane / negative regulation of cell population proliferation / heme binding / positive regulation of gene expression / Golgi apparatus / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Li, H. / Poulos, T.L. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6pp3.cif.gz | 682 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6pp3.ent.gz | 564.5 KB | Display | PDB format |
PDBx/mmJSON format | 6pp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pp3_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6pp3_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 6pp3_validation.xml.gz | 68.9 KB | Display | |
Data in CIF | 6pp3_validation.cif.gz | 93 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/6pp3 ftp://data.pdbj.org/pub/pdb/validation_reports/pp/6pp3 | HTTPS FTP |
-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 6po8C 6po9C 6poaC 6pobC 6pocC 6potC 6pouC 6povC 6powC 6poxC 6poyC 6pozC 6pp0C 6pp1C 6pp2C 6pp4C 4d1pS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 49345.770 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: endothelial / Gene: NOS3 / Plasmid: pCWori / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29474, nitric-oxide synthase (NADPH) |
---|
-Non-polymers , 9 types, 558 molecules
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-H4B / #4: Chemical | ChemComp-OS7 / #5: Chemical | ChemComp-BTB / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-CL / #9: Chemical | ChemComp-GD / #10: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.3 % / Description: rods |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10-12% PEG3350, 0.1M BIS-TRIS 0.2-0.3M MG ACETATE, 0.1M GdCl3 10% glycerol, 5 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2018 / 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: 1.95→60 Å / Num. obs: 140683 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.102 / Rsym value: 0.16 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 2.448 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 6939 / CC1/2: 0.327 / Rpim(I) all: 1.619 / Rsym value: 2.448 / % possible all: 99.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4D1P Resolution: 1.95→49.862 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.66 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→49.862 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|