Structure-based mutation analysis BCKDHA
From Bioinformatikpedia
Contents
Structure selection
The following table presents the PDB structures for BCKDHA to date:
| PDB id | resolution [Å] | R-factor | coverage | ph-value |
|---|---|---|---|---|
| 1DTW | 2.70 | 0.224 | 7.5* | |
| 1OLS | 1.85 | 0.172 | 5.5 | |
| 1OLU | 1.90 | 0.161 | 5.5 | |
| 1OLX | 2.25 | 0.161 | 5.5 | |
| 1U5B | 1.83 | 0.156 | 5.8 | |
| 1V11 | 1.95 | 0.139* | 5.5 | |
| 1V16 | 1.90 | 0.132* | 5.5 | |
| 1V1M | 2.00 | 0.130* | 5.5 | |
| 1V1R | 1.80 | 0.158 | 5.5 | |
| 1WCI | 1.84 | 0.149 | 5.5 | |
| 1X7W | 1.73 | 0.148 | 5.8 | |
| 1X7X | 2.10 | 0.149 | 5.8 | |
| 1X7Y | 1.57 | 0.150 | 5.8 | |
| 1X7Z | 1.72 | 0.154 | 5.8 | |
| 1X80 | 2.00 | 0.161 | 5.8 | |
| 2BEU | 1.89 | 0.171 | 5.5 | |
| 2BEV | 1.80 | 0.139 | 5.5 | |
| 2BEW | 1.79 | 0.147 | 5.5 | |
| 2BFB | 1.77 | 0.145 | 5.5 | |
| 2BFC | 1.64 | 0.144 | 5.5 | |
| 2BFD | 1.39* | 0.150 | 5.5 | |
| 2BFE | 1.69 | 0.150 | 5.5 | |
| 2BFF | 1.46 | 0.150 | 5.5 | |
| 2J9F | 1.88 | 0.171 | 5.5 |
The following PDB Structure was chosen because of its good experimental resolution: <bold></bold>
- resultion:
- R-factor
- ph-value
Comparison energies
Mapping of the mutations on thw crystal structure
SCWRL
Before we could use SCWRL we first had to get the sequence of our model: repairPDB bckdha.pdb -seq >> bckdha.seq
When we have the sequence we have to make one file for each mutation. In these files we copied the bckdha.seq and changed the sequence to lower case letters. Then we add the mutation in an upper case letter.
To run SCWRL we used the command: scwrl -i bckdha.pdb -s mutation1.seq -o mutation1Model.pdb
foldX
gromacs
Gromacs
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