[English] 日本語
Yorodumi- PDB-1dd7: MURINE INDUCIBLE NITRIC OXIDE SYNTHASE OXYGENASE DOMAIN (DELTA 11... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dd7 | ||||||
---|---|---|---|---|---|---|---|
Title | MURINE INDUCIBLE NITRIC OXIDE SYNTHASE OXYGENASE DOMAIN (DELTA 114) (N-[(1,3-BENZODIOXOL-5-YL)METHYL]-1-[2-(1H-IMIDAZOL-1-YL)PYRIMIDIN-4-YL]-4-(METHOXYCARBONYL)-PIPERAZINE-2-ACETAMIDE COMPLEX | ||||||
Components | INDUCIBLE NITRIC OXIDE SYNTHASENitric oxide synthase | ||||||
Keywords | OXIDOREDUCTASE / NITRIC OXIDE / L-ARGININE MONOOXYGENASE / HEME / DIMERIZATION / INHIBITOR / NOS | ||||||
Function / homology | Function and homology information Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / Peroxisomal protein import / cAMP-dependent protein kinase regulator activity / prostaglandin secretion / positive regulation of killing of cells of another organism / tetrahydrobiopterin binding / arginine binding / cortical cytoskeleton ...Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / Peroxisomal protein import / cAMP-dependent protein kinase regulator activity / prostaglandin secretion / positive regulation of killing of cells of another organism / tetrahydrobiopterin binding / arginine binding / cortical cytoskeleton / superoxide metabolic process / cGMP-mediated signaling / nitric-oxide synthase binding / cellular response to cytokine stimulus / regulation of cytokine production involved in inflammatory response / peptidyl-cysteine S-nitrosylation / regulation of insulin secretion / cellular response to organic cyclic compound / nitric-oxide synthase (NADPH) / blood vessel remodeling / response to tumor necrosis factor / nitric-oxide synthase activity / nitric oxide mediated signal transduction / arginine catabolic process / negative regulation of blood pressure / nitric oxide biosynthetic process / response to hormone / positive regulation of interleukin-8 production / response to bacterium / Hsp90 protein binding / negative regulation of protein catabolic process / beta-catenin binding / regulation of blood pressure / peroxisome / positive regulation of interleukin-6 production / cellular response to type II interferon / circadian rhythm / cellular response to xenobiotic stimulus / FMN binding / flavin adenine dinucleotide binding / NADP binding / actin binding / regulation of cell population proliferation / cellular response to lipopolysaccharide / response to lipopolysaccharide / response to hypoxia / calmodulin binding / intracellular signal transduction / defense response to bacterium / cadherin binding / inflammatory response / positive regulation of apoptotic process / negative regulation of gene expression / heme binding / protein kinase binding / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 Å | ||||||
Authors | Adler, M. / Whitlow, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Allosteric inhibitors of inducible nitric oxide synthase dimerization discovered via combinatorial chemistry. Authors: McMillan, K. / Adler, M. / Auld, D.S. / Baldwin, J.J. / Blasko, E. / Browne, L.J. / Chelsky, D. / Davey, D. / Dolle, R.E. / Eagen, K.A. / Erickson, S. / Feldman, R.I. / Glaser, C.B. / ...Authors: McMillan, K. / Adler, M. / Auld, D.S. / Baldwin, J.J. / Blasko, E. / Browne, L.J. / Chelsky, D. / Davey, D. / Dolle, R.E. / Eagen, K.A. / Erickson, S. / Feldman, R.I. / Glaser, C.B. / Mallari, C. / Morrissey, M.M. / Ohlmeyer, M.H. / Pan, G. / Parkinson, J.F. / Phillips, G.B. / Polokoff, M.A. / Sigal, N.H. / Vergona, R. / Whitlow, M. / Young, T.A. / Devlin, J.J. #1: Journal: Science / Year: 1997 Title: The Structure of Nitric Oxide Synthase Oxygenase Domain and Inhibitor Complexes Authors: Crane, B.R. / Arvai, A.S. / Gachhui, R. / Wu, C. / Ghosh, D.K. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A. #2: Journal: Biochemistry / Year: 1997 Title: Characterization of the Inducible Nitric Oxide Synthase Oxygenase Domain Identifies a 49 Amino Acid Segment Required for Subunit Dimerization and Tetrahydrobiopterin Interaction Authors: Ghosh, D.K. / Wu, C. / Pitters, E. / Moloney, M. / Werner, E.R. / Mayer, B. / Stuehr, D.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dd7.cif.gz | 98.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dd7.ent.gz | 78 KB | Display | PDB format |
PDBx/mmJSON format | 1dd7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/1dd7 ftp://data.pdbj.org/pub/pdb/validation_reports/dd/1dd7 | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer |
-Components
#1: Protein | Mass: 45270.379 Da / Num. of mol.: 1 / Fragment: OXYGENASE DOMAIN 114-498 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PCWORI / Production host: Escherichia coli (E. coli) / References: UniProt: P29477, nitric-oxide synthase (NADPH) |
---|---|
#2: Chemical | ChemComp-SO3 / |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-1PM / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.24 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: Crystals of murine delta114 iNOS were prepared in the presence of imidazole following the procedures of Crane et al. (reference 1) as follows: The 6 uL crystallization drops contained 20 ...Details: Crystals of murine delta114 iNOS were prepared in the presence of imidazole following the procedures of Crane et al. (reference 1) as follows: The 6 uL crystallization drops contained 20 mg/ml murine delta114 iNOS, 20 mM HEPES pH 7.6, 5 % glycerol, 0.5 mM DTT, 6.8 % PEG-3350, 60 mM Na2SO3, and 50 mM imidazole/malate buffer pH 4.7 were placed over a 1 ml reservoir containing 13.6 % PEG-3350, 120 mM Na2SO3, and 100 mM imidazole/malate buffer pH 4.7. These crystals were soaked for 25 hours in 5 uM N-[(1,3-benzodioxol-5-yl)methyl]-1-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]- 4-(methoxycarbonyl)-piperazine-2-acetamide, 14 % PEG-3350, 1 mM NaN3, 50 mM MES pH 6.5 and 50 mM Na2SO3. The crystals were then rinsed in 33 % ethylene glycol, 9.3% PEG-3350, 0.7 mM NaN3, 33 mM MES pH 6.5 and 33 mM Na2SO3, and flash frozen in liquid nitrogen. , VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 32 ℃ / pH: 6.5 / Method: vapor diffusion / Details: Crane, B.R., (1997) Science, 278, 425. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 27, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→19.8 Å / Num. all: 70075 / Num. obs: 21034 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.25→2.31 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.643 / Num. unique all: 1420 / % possible all: 89 |
Reflection | *PLUS Num. measured all: 70075 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.25→8 Å / σ(F): 2 / σ(I): 0 Stereochemistry target values: R. A. Engh and R. Huber, Acta Cryst. Sect. A., 1991 Details: Simulated annealing from 600 degrees K followed by minimization and B factor refinement.
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→8 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.197 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |