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Yorodumi- PDB-6wxz: CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH... -
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-Basic information
Entry | Database: PDB / ID: 6wxz | ||||||
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Title | CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-29 A.K.A 7-(1,2-DIPHENYLETHYL)-1H-[1,2,3]TRIAZOLO[4,5-B]PYRIDIN-5-AMINE | ||||||
Components | (Myeloperoxidase ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / MYELOPEROXIDASE / MPO / HEME | ||||||
Function / homology | Function and homology information 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 / peroxidase activity / defense response / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.226 Å | ||||||
Authors | Khan, J.A. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wxz.cif.gz | 495.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wxz.ent.gz | 406.1 KB | Display | PDB format |
PDBx/mmJSON format | 6wxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wxz_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 6wxz_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 6wxz_validation.xml.gz | 47.8 KB | Display | |
Data in CIF | 6wxz_validation.cif.gz | 66.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/6wxz ftp://data.pdbj.org/pub/pdb/validation_reports/wx/6wxz | HTTPS FTP |
-Related structure data
Related structure data | 6wy0C 6wy5C 6wy7C 6wydC 5qj2S S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
-Myeloperoxidase ... , 2 types, 4 molecules ADBE
#1: Protein | Mass: 11974.420 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: Blood Neutrophill / References: UniProt: P05164, myeloperoxidase #2: Protein | Mass: 53321.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase |
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-Sugars , 4 types, 14 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / #10: Sugar | |
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-Non-polymers , 5 types, 442 molecules
#5: Chemical | ChemComp-CL / #6: Chemical | #8: Chemical | #9: Chemical | #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.65 Å3/Da / Density % sol: 53.55 % |
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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: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
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: 2.226→239.63 Å / Num. obs: 69646 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 48.36 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2.226→2.35 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1391 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5QJ2 Resolution: 2.226→98.02 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.267 / Data cutoff high absF: 17600 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.276 / SU Rfree Blow DPI: 0.203 / SU Rfree Cruickshank DPI: 0.202
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Displacement parameters | Biso max: 139.11 Å2 / Biso mean: 58.81 Å2 / Biso min: 30.35 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.226→98.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.23→2.24 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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