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Yorodumi- PDB-4cu1: Structure of bovine endothelial nitric oxide synthase heme domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cu1 | ||||||
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Title | Structure of bovine endothelial nitric oxide synthase heme domain in complex with 6-[(2S)-3-amino-2-{5-[2-(6-amino-4-methylpyridin-2-yl)ethyl]pyridin-3-yl}propyl]-4-methylpyridin-2-amine | ||||||
Components | (NITRIC OXIDE SYNTHASE, ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information cellular response to laminar fluid shear stress / positive regulation of guanylate cyclase activity / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / nitric oxide mediated signal transduction / nitric-oxide synthase activity / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric oxide biosynthetic process / negative regulation of blood pressure ...cellular response to laminar fluid shear stress / positive regulation of guanylate cyclase activity / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / nitric oxide mediated signal transduction / nitric-oxide synthase activity / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric oxide biosynthetic process / negative regulation of blood pressure / response to hormone / mitochondrion organization / caveola / blood coagulation / FMN binding / NADP binding / flavin adenine dinucleotide binding / response to lipopolysaccharide / calmodulin binding / cytoskeleton / heme binding / Golgi apparatus / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.89 Å | ||||||
Authors | Li, H. / Poulos, T.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Nitric Oxide Synthase Inhibitors that Interact with Both a Heme Propionate and Tetrahydrobiopterin Show High Isoform Selectivity. Authors: Kang, S. / Tang, W. / Li, H. / 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 | 4cu1.cif.gz | 339.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cu1.ent.gz | 286.8 KB | Display | PDB format |
PDBx/mmJSON format | 4cu1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cu1_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4cu1_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4cu1_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 4cu1_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/4cu1 ftp://data.pdbj.org/pub/pdb/validation_reports/cu/4cu1 | HTTPS FTP |
-Related structure data
Related structure data | 4ctpC 4ctqC 4ctrC 4cttC 4ctuC 4ctvC 4ctwC 4ctxC 4ctyC 4ctzC 4cu0C 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
-NITRIC OXIDE SYNTHASE, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 49727.012 Da / Num. of mol.: 1 / Fragment: HEME DOMAIN, RESIDUES 40-482 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29473, nitric-oxide synthase (NADPH) |
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#2: Protein | Mass: 49623.027 Da / Num. of mol.: 1 / Fragment: HEME DOMAIN, RESIDUES 40-482 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29473, nitric-oxide synthase (NADPH) |
-Non-polymers , 7 types, 306 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-ZN / | #9: 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: 2.5 Å3/Da / Density % sol: 50.7 % / Description: NONE |
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Crystal grow | pH: 6 Details: 20-22% PEG3350, 0.1 M CACODYLATE, 150-200 MM MG ACETATE, 5 MM TCEP, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 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: 1.9→50 Å / Num. obs: 74481 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.2 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.89→87.04 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 7.018 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 110 TO 120 IN BOTH CHAIN A AND CHAIN B ARE DISORDERED. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.015 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→87.04 Å
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Refine LS restraints |
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