Difference between revisions of "Structure-based mutation analysis (PKU)"
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== 1J8U == |
== 1J8U == |
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IN order to know the structure of the protein and its important residues, we have a look at its structure with PyMol and visualize the BH4 and the Fe-ion with the most important residues. |
IN order to know the structure of the protein and its important residues, we have a look at its structure with PyMol and visualize the BH4 and the Fe-ion with the most important residues. |
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<figure id="1J8Uwhole">[[File:1J8Usites.png|500px|thumb|<caption>Rendering of the overall structures of 1J8U using PyMol. The protein is colored cyan overall, whereas the Fe-atom is colored red and the important residues are shown as sticks and colored in the element-based fashion. Binding is shown with yellow strokes, if the distance is bigger than 1.5 Å</caption>]] </figure> |
<figure id="1J8Uwhole">[[File:1J8Usites.png|500px|thumb|<caption>Rendering of the overall structures of 1J8U using PyMol. The protein is colored cyan overall, whereas the Fe-atom is colored red and the important residues are shown as sticks and colored in the element-based fashion. Binding is shown with yellow strokes, if the distance is bigger than 1.5 Å</caption>]] </figure> |
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| − | <figure id="1J8Uclose">[[File:1J8Usitesclose.png|500px|thumb|<caption>Rendering of a close-up of the structures of 1J8U using PyMol. The protein is colored cyan overall, whereas the Fe-atom is colored red and the important residues are shown as sticks and colored in the element-based fashion. Binding is shown with yellow strokes, if the distance is bigger than 1.5 Å</caption>]] </figure> |
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| + | <div style="float: left; width: 50%"> |
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| + | <figure id="1J8Uclose">[[File:1J8Usitesclose.png|500px|thumb|left|<caption>Rendering of a close-up of the structures of 1J8U using PyMol. The protein is colored cyan overall, whereas the Fe-atom is colored red and the important residues are shown as sticks and colored in the element-based fashion. Binding is shown with yellow strokes, if the distance is bigger than 1.5 Å</caption>]] </figure> |
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Revision as of 14:03, 18 June 2012
short task description
Finding the right structure
As proposed we searched the UNIProt entry for our protein and then selected the entry with the highest resolution and the lowest r-Value. In our case this is 1J8U which is the protein in a complex with its cosubstrate BH4. IN the following we will only use this structure, but we also list the results we found. <figtable id="uniprotresult">
| Entry | Method | Resolution (Å) | r-Value | Chain | Positions | PDBsum |
|---|---|---|---|---|---|---|
| 1DMW | X-ray | 2.00 | 0.200 | A | 118-424 | [»] |
| 1J8T | X-ray | 1.70 | 0.197 | A | 103-427 | [»] |
| 1J8U | X-ray | 1.50 | 0.157 | A | 103-427 | [»] |
| 1KW0 | X-ray | 2.50 | 0.220 | A | 103-427 | [»] |
| 1LRM | X-ray | 2.10 | 0.211 | A | 103-427 | [»] |
| 1MMK | X-ray | 2.00 | 0.199 | A | 103-427 | [»] |
| 1MMT | X-ray | 2.00 | 0.213 | A | 103-427 | [»] |
| 1PAH | X-ray | 2.00 | 0.176 | A | 117-424 | [»] |
| 1TDW | X-ray | 2.10 | 0.206 | A | 117-424 | [»] |
| 1TG2 | X-ray | 2.20 | 0.213 | A | 117-424 | [»] |
| 2PAH | X-ray | 3.10 | 0.251 | A/B | 118-452 | [»] |
| 3PAH | X-ray | 2.00 | 0.175 | A | 117-424 | [»] |
| 4ANP | X-ray | 2.11 | 0.204 | A | 104-427 | [»] |
| 4PAH | X-ray | 2.00 | 0.169 | A | 117-424 | [»] |
| 5PAH | X-ray | 2.10 | 0.163 | A | 117-424 | [»] |
| 6PAH | X-ray | 2.15 | 0.171 | A | 117-424 | [»] |
</figtable> In <xr id="uniprotresult"/> there are all results according to which we selected 1J8U to be our reference for this weeks task. The corresponding line is marked in yellow.
1J8U
IN order to know the structure of the protein and its important residues, we have a look at its structure with PyMol and visualize the BH4 and the Fe-ion with the most important residues.
<figure id="1J8Uwhole"> </figure>
<figure id="1J8Uclose"> </figure>
