Difference between revisions of "Part:BBa K4165085"

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===Dry-Lab Characterization===
 
===Dry-Lab Characterization===
  
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===PDB Structure===
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<p style=" font-weight: bold; font-size:14px;"> Quality Assessment </p>
  
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It has a predicted sturcture (AlphaFold2)
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<p> C-beta deviation: 0 </p>
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<p> Clash score: 50.77 </p>
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<p> Molprobity: 3.2 </p>
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AlphaFold:
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<p> Ramachandran favored: 78.95 </p>
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https://alphafold.ebi.ac.uk/entry/Q6IE38
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<p> Ramachandran outliers: 8.42 </p>
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Molprobity:  
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<p> QMean_4: -3.71517 </p>
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Clash Score:
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<p> QMean_6: -3.3123 </p>
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Ramachandran Favoured:  
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Ramachandran Outliers:  
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Rotamers Outliers:  
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C-beta Deviations:
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Q-Mean:  
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<p style=" font-weight: bold; font-size:14px;"> Modelling </p>
  
  
 
<html>
 
<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/switches/5-alphafold.png" style="margin-left:200px;" alt="" width="500" /></p>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-inhibitors/model4-alphafold.png" style="margin-left:200px;" alt="" width="500" /></p>
 
</html>
 
</html>
  
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                   Figure 1.: A graphical illustration showing the structure of the inhibitor (AlphaFold).
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                   Figure 1.: A graphical illustration showing the structure of the inhibitor (Model 4-AlphaFold).
  
  
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<p style=" font-weight: bold; font-size:14px;"> Docking </p>
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<p> Gibbs Free Energy is -37.794 </p>
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<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-inhibitors/dry-lab/dock-q6ie38.png" style="margin-left:200px;" alt="" width="500" /></p>
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</html>
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                  Figure 2.: A graphical illustration showing the binding of the inhibitor with HtrA1 (Galaxy).
  
 
===Reference:===
 
===Reference:===

Revision as of 01:40, 12 October 2022


SPINK14 (Serine Peptidase Inhibitor Kazal type 14).

This basic part encodes Human serine protease inhibitor known as SPINK14 which is able to inhibit trypsin-like proteases, like HtrA1 (BBa_K4165004).



Usage and Biology

This type of family encodes for a type of inhibitor that is predicted to be able to inhibit serine peptidases. The inhibitor is present extracellularly. The inhibitor binds to trypsin-like proteases (serine proteases) and since the catalytic core of HtrA1 (BBa_K4165004) is considered as a trypsin-like catalytic domain, so this inhibitor also is considered to inhibit the function of HtrA1 [1-3].

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Dry-Lab Characterization

Quality Assessment

C-beta deviation: 0

Clash score: 50.77

Molprobity: 3.2

Ramachandran favored: 78.95

Ramachandran outliers: 8.42

QMean_4: -3.71517

QMean_6: -3.3123

Modelling 


                 Figure 1.: A graphical illustration showing the structure of the inhibitor (Model 4-AlphaFold).


Docking

Gibbs Free Energy is -37.794 


                 Figure 2.: A graphical illustration showing the binding of the inhibitor with HtrA1 (Galaxy).

Reference:

1 - Frochaux, V., Hildebrand, D., Talke, A., Linscheid, M. W., & Schlüter, H. (2014). Alpha-1-antitrypsin: a novel human high temperature requirement protease A1 (HTRA1) substrate in human placental tissue. PloS one, 9(10), e109483.
2 - Grau, S., Baldi, A., Bussani, R., Tian, X., Stefanescu, R., Przybylski, M., ... & Ehrmann, M. (2005). Implications of the serine protease HtrA1 in amyloid precursor protein processing. Proceedings of the National Academy of Sciences, 102(17), 6021-6026.
3 - Eigenbrot, C., Ultsch, M., Lipari, M. T., Moran, P., Lin, S. J., Ganesan, R., ... & Kirchhofer, D. (2012). Structural and functional analysis of HtrA1 and its subdomains. Structure, 20(6), 1040-1050.