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- PDB-6wyd: CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH... -
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Basic information
Entry | Database: PDB / ID: 6wyd | ||||||
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Title | CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-12 (AKA; 7-benzyl-1H-[1,2,3]triazolo[4,5-b]pyrid | ||||||
![]() | (Myeloperoxidase ...) x 2 | ||||||
![]() | OXIDOREDUCTASE / MYELOPEROXIDASE | ||||||
Function / homology | ![]() myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / respiratory burst involved in defense response / low-density lipoprotein particle remodeling / response to food / azurophil granule ...myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / respiratory burst involved in defense response / low-density lipoprotein particle remodeling / response to food / azurophil granule / defense response to fungus / response to mechanical stimulus / removal of superoxide radicals / secretory granule / hydrogen peroxide catabolic process / defense response / peroxidase activity / azurophil granule lumen / heparin binding / response to oxidative stress / response to lipopolysaccharide / lysosome / defense response to bacterium / intracellular membrane-bounded organelle / chromatin binding / heme binding / Neutrophil degranulation / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Khan, J.A. | ||||||
![]() | ![]() Title: Discovery and structure activity relationships of 7-benzyl triazolopyridines as stable, selective, and reversible inhibitors of myeloperoxidase. Authors: Shaw, S.A. / Vokits, B.P. / Dilger, A.K. / Viet, A. / Clark, C.G. / Abell, L.M. / Locke, G.A. / Duke, G. / Kopcho, L.M. / Dongre, A. / Gao, J. / Krishnakumar, A. / Jusuf, S. / Khan, J. / ...Authors: Shaw, S.A. / Vokits, B.P. / Dilger, A.K. / Viet, A. / Clark, C.G. / Abell, L.M. / Locke, G.A. / Duke, G. / Kopcho, L.M. / Dongre, A. / Gao, J. / Krishnakumar, A. / Jusuf, S. / Khan, J. / Spronk, S.A. / Basso, M.D. / Zhao, L. / Cantor, G.H. / Onorato, J.M. / Wexler, R.R. / Duclos, F. / Kick, E.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 470.3 KB | Display | ![]() |
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PDB format | ![]() | 384.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
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Full document | ![]() | 3.1 MB | Display | |
Data in XML | ![]() | 90.6 KB | Display | |
Data in CIF | ![]() | 119.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wxzC ![]() 6wy0C ![]() 6wy5C ![]() 6wy7C ![]() 6qj2S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Myeloperoxidase ... , 2 types, 8 molecules ADFHBEGI
#1: Protein | Mass: 11974.420 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 53305.266 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 4 types, 35 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/FUC.gif)
![](data/chem/img/BMA.gif)
![](data/chem/img/MAN.gif)
![](data/chem/img/FUC.gif)
![](data/chem/img/BMA.gif)
![](data/chem/img/MAN.gif)
#4: Sugar | ChemComp-NAG / #5: Sugar | ChemComp-FUC / #7: Sugar | ChemComp-BMA / #8: Sugar | ChemComp-MAN / |
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-Non-polymers , 5 types, 280 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/7GD.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/7GD.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CL / #6: Chemical | ChemComp-HEC / #9: Chemical | ChemComp-7GD / #10: Chemical | ChemComp-CA / #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.64 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 0.1M Hepes pH 7.5, 150mM NaCl, 20-25%(V/V)PEG3350.Crystals were cryoprotected by supplementing the mother liquor with 15% (v/v) ethylene glycol and harvested by flash-cooling in liquid nitrogen PH range: 7.5? |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→200 Å / Num. obs: 82041 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 62.29 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.55→2.68 Å / Redundancy: 7 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 5972 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6QJ2 Resolution: 2.55→115.53 Å / Cor.coef. Fo:Fc: 0.9357 / Cor.coef. Fo:Fc free: 0.8939 / SU R Cruickshank DPI: 0.824 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.732 / SU Rfree Blow DPI: 0.301 / SU Rfree Cruickshank DPI: 0.309
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Displacement parameters | Biso max: 128.16 Å2 / Biso mean: 50.55 Å2 / Biso min: 13.98 Å2
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Refine analyze | Luzzati coordinate error obs: 0.322 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.55→115.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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