[English] 日本語
![](img/lk-miru.gif)
- PDB-7lan: CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7lan | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH COMPOUND-30 AKA 7-[(3~{S},4~{R},6~{R})-4-benzyl-2-oxa-7,13,14-triazatetracyclo[14.3.1.1^{3,6}.1^{11,14}]docosa-1(19),11(21),12,16(20),17-pentaen-10-yl]-3~{H}-triazolo[4,5-b]pyridin-5-amine | ||||||
![]() |
| ||||||
![]() | 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 / 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 / heme binding / chromatin 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: Small molecule and macrocyclic pyrazole derived inhibitors of myeloperoxidase (MPO). Authors: Hu, C.H. / Neissel Valente, M.W. / Halpern, O.S. / Jusuf, S. / Khan, J.A. / Locke, G.A. / Duke, G.J. / Liu, X. / Duclos, F.J. / Wexler, R.R. / Kick, E.K. / Smallheer, J.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 494.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 403.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7laeC ![]() 7lagC ![]() 7lalC ![]() 6wy7S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 2 types, 8 molecules ADFHBEGI
#1: Protein | Mass: 11974.420 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Blood Neutrophill / Source: (natural) ![]() #2: Protein | Mass: 53218.188 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|
-Sugars , 3 types, 12 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
---|
-Non-polymers , 5 types, 982 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/XS1.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/XS1.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-HEM / #8: Chemical | ChemComp-CA / #9: Chemical | ChemComp-XS1 / #10: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.78 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→50 Å / Num. obs: 114459 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.8 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.28→2.36 Å / Rmerge(I) obs: 0.72 / Num. unique obs: 11351 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6WY7 Resolution: 2.28→47.45 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.9253 / SU R Cruickshank DPI: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.343 / SU Rfree Blow DPI: 0.224 / SU Rfree Cruickshank DPI: 0.226
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 117.94 Å2 / Biso mean: 44.53 Å2 / Biso min: 5.91 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.293 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.28→47.45 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.28→2.34 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|