Structure-based mutation analysis (Phenylketonuria)
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Summary
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Preparation
In the further analysis we used the protein structure of 2PAH for the analysis. Now, we will use 1J8U since this structure got better results for the following observed constraints:
- Structure with the highest resolution (small Å value)
- Smallest R-factor
- Highest coverage
- pH-value ideally near physiological pH of 7.4
- No gaps (missing residues) included in the structure, so a consecutive numbering of residues should be given
To proof our statement, the results of the constraints of 2PAH and 1J8U are compared in the Table below.
| Protein | Resolution(Å) | R-factor | pH | gaps | chain | Positions in P00439 | Coverage % |
|---|---|---|---|---|---|---|---|
| 1DMW | 2.00 | 0.20 | 6.80 | x | A | 118-424 | x |
| 1J8T | 1.70 | 0.20 | 6.80 | x | A | 103-427 | x |
| 1J8U | 1.50 | 0.16 | 6.80 | 0 | A | 103-427 | 71.68 |
| 1KW0 | 2.50 | 0.22 | 6.80 | x | A | 103-427 | x |
| 1LRM | 2.10 | 0.21 | 6.80 | x | A | 103-427 | x |
| 1MMK | 2.00 | 0.20 | 6.80 | x | A | 103-427 | x |
| 1MMT | 2.00 | 0.21 | 6.80 | x | A | 103-427 | x |
| 1PAH | 2.00 | 0.18 | 6.80 | x | A | 117-424 | x |
| 1TDW | 2.10 | 0.21 | 6.80 | x | A | 117-424 | x |
| 1TG2 | 2.20 | 0.21 | 6.80 | x | A | 117-424 | x |
| 2PAH | 3.10 | 0.25 | 7.00 | x | A/B | 118-452 | 73.89 |
| 3PAH | 2.00 | 0.18 | 6.80 | x | A | 117-424 | x |
| 4ANP | 2.11 | 0.20 | 6.80 | x | A | 104-427 | x |
| 4PAH | 2.00 | 0.17 | 6.80 | x | A | 117-424 | x |
| 5PAH | 2.10 | 0.16 | 6.80 | x | A | 117-424 | x |
| 6PAH | 2.15 | 0.17 | 6.80 | x | A | 117-424 | x |
Energy comparisons
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FoldX
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Minimise
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References
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