Glucocerebrosidase homology modelling
Contents
Homologous Structures
The 10 best results of the sequence search with HHSearch (as retrieved in Task 1) are listed in the table below.
| > 60% sequence identity | ||||
| PDB-ID | name | identity | organism | template |
| 2nt0 | Glucosylceramidase | Homo Sapiens | 99% | |
| > 40% sequence identity | ||||
| PDB-ID | name | identity | organism | template |
| > 0% sequence identity | ||||
| PDB-ID | name | identity | organism | template |
| 2wnw | SrfJ | Salmonella enterica subsp. enterica | 29% | x |
| 3clw | conserved exported protein | Bacteroides fragilis | 13% | |
| 3kl0 | Glucuronoxylan Xylanohydrolase | Bacillus subtilis | 18% | x |
| 1nof | xylanase | Erwinia chrysanthemi | 18% | |
| 2e4t | Endoglucanase | Clostridium thermocellum | 11% | x |
| 3ii1 | Cellulase | Uncultured bacterium | 15% | |
| 1qw9 | Arabinosidase | Geobacillus stearothermophilus | 13% | |
| 1ik2 | Endoglucanase | Clostridium acetobutylicum | 12 % | |
| 2c7f | alpha-L-Arabinofuranosidase | Clostridium thermocellum | 16% | |
Calculation of Models
MODELLER
iTasser
SWISS-MODEL
SWISS-MODEL workspace was published by Arnold et al. in 2005. <ref> Arnold K., Bordoli L., Kopp J., and Schwede T. (2006). The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics, 22,195-201.</ref>
Usage - Automated Mode
- Webserver: http://swissmodel.expasy.org/workspace/index.php?func=modelling_simple1
- Input: Sequence in fasta format
The automated mode should only be used, if target and template share more than 50% of sequence identity. This is not the case for the proteins selected as target in this case. Therefore the Alignment Mode will be used to create the models for glucocerebrosidase.
Usage - Alignment Mode
- Webserver: http://swissmodel.expasy.org/workspace/index.php?func=modelling_align1
- Input: Target-Template Alignment in different formats (FASTA, CLUSTALW, ...)
2WNW
To use the Alignment Mode of Swiss-Model, a alignment had to be created. To create the alignment clustalw was used. The resulting alignment was than used for the Alignment Mode. The workunit was aborted however, as there were too many unfruitful attempts to rebuild a loop. This indicates, that the alignment is not good and that it has to be adjusted.
References
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