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- PDB-1dm7: BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dm7 | ||||||
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Title | BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WITH HOMOARGININE (H4B FREE) | ||||||
![]() | NITRIC OXIDE SYNTHASE | ||||||
![]() | OXIDOREDUCTASE / ALPHA-BETA FOLD | ||||||
Function / homology | ![]() 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 / cytoskeleton / calmodulin binding / heme binding / Golgi apparatus / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Raman, C.S. / Li, H. / Martasek, P. / Southan, G.J. / Masters, B.S.S. / Poulos, T.L. | ||||||
![]() | ![]() Title: Crystal Structures of Bovine Endothelial Nitric Oxide Synthase Heme Domain Complexed With Various Inhibitors Authors: Raman, C.S. / Li, H. / Martasek, P. / Southan, G.J. / Masters, B.S.S. / Poulos, T.L. #1: ![]() Title: Crystal Structure of Constitutive Endothelial Nitric Oxide Synthase: A Paradigm for Pterin Function Involving a Novel Metal Center Authors: Raman, C.S. / Li, H. / Martasek, P. / Kral, V. / Masters, B.S.S. / Poulos, T.L. #2: ![]() Title: Structure of Nitric Oxide Synthase Oxygenase Dimer with Pterin and Substrate Authors: Crane, B.R. / Arvai, A.S. / Ghosh, D.K. / Wu, C. / Getzoff, E.D. / Stuehr, D.J. / Tainer, A. #3: ![]() Title: Efficient Formation of Nitric Oxide from Selective Oxidation of N-Aryl N'- Hydroxyguanidines by Inducible Nitric Oxide Synthase Authors: Renodon-Corniere, A. / Boucher, J.-L. / Dijols, S. / Stuehr, D.J. / Mansuy, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192.8 KB | Display | ![]() |
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PDB format | ![]() | 150.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 49710.105 Da / Num. of mol.: 2 / Fragment: HEME DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 423 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HRG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HRG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-ZN / | #8: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | ZN ION SITS RIGHT ON THE NCS 2-FOLD THAT DEFINES THE DIMER INTERFACE AND IS COORDINATED ...ZN ION SITS RIGHT ON THE NCS 2-FOLD THAT DEFINES THE DIMER INTERFACE AND IS COORDINATE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.97 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 4000, CACODYLATE, MAGNESIUM ACETATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 66766 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.1→2.24 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.47 / % possible all: 96.7 |
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Processing
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Refinement | Resolution: 2.1→28.4 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2579569.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: RESIDUES 39 TO 66 OF MOLECULE A AND RESIDUES 39 TO 68 IN MOLECULE B ARE NOT VISIBLE IN THE ELECTRON DENSITY. RESIDUES 108-120 ARE DISORDERED, BUT THE TENTATIVE MODEL WAS INCLUDED IN THE REFINEMENT.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.8 Å2 / ksol: 0.363 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→28.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
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