Difference between revisions of "Structure-based mutation analysis (PKU)"

From Bioinformatikpedia
(→‎Finding the right structure)
(→‎Finding the right structure)
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As proposed we searched the [http://www.uniprot.org/uniprot/P00439 UNIProt entry] for our protein and then selected the entry with the highest resolution and the lowest r-Value. In our case this is [http://www.ebi.ac.uk/pdbe-srv/view/entry/1J8U 1J8U] which is the protein in a complex with its cosubstrate [http://en.wikipedia.org/wiki/Tetrahydrobiopterin BH4].
  
As proposed we searched the [http://www.uniprot.org/uniprot/P00439 UNIProt entry] for our protein and then selected the entry with the highest resolution and the lowest r-Value. In our case this is [http://www.ebi.ac.uk/pdbe-srv/view/entry/1J8U 1J8U] which is the protein in a complex with its cosubstrate [http://en.wikipedia.org/wiki/Tetrahydrobiopterin BH4].
 
IN the following we will only use this structure, but we also list the results we found.
  
IN the following we will only use this structure, but we also list the results we found.
−
When we checked for structures which are known for P00439 (PheOH) in the PDB we found several, of which we just used the one with the lowest Å- and r-Value.
  
 
<figtable id="uniprotresult">
  
<figtable id="uniprotresult">
 
<center><caption>Table with results from UNIProt with r-Value inserted</caption></center>
  
<center><caption>Table with results from UNIProt with r-Value inserted</caption></center>
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|X-ray
  
|X-ray
 
|2.00
  
|2.00
  +
|0.200
−
|
  
 
|A
  
|A
 
|[http://www.uniprot.org/blast/?about=P00439%5B118-424%5D 118-424]
  
|[http://www.uniprot.org/blast/?about=P00439%5B118-424%5D 118-424]
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|X-ray
  
|X-ray
 
|1.70
  
|1.70
  +
|0.197
−
|
  
 
|A
  
|A
 
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
  
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
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|X-ray
  
|X-ray
 
|1.50
  
|1.50
  +
|0.157
−
|
  
 
|A
  
|A
 
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
  
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
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|X-ray
  
|X-ray
 
|2.50
  
|2.50
  +
|0.220
−
|
  
 
|A
  
|A
 
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
  
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
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|X-ray
  
|X-ray
 
|2.10
  
|2.10
  +
|0.211
−
|
  
 
|A
  
|A
 
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
  
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
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|X-ray
  
|X-ray
 
|2.00
  
|2.00
  +
|0.199
−
|
  
 
|A
  
|A
 
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
  
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
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|X-ray
  
|X-ray
 
|2.00
  
|2.00
  +
|0.213
−
|
  
 
|A
  
|A
 
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
  
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
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|X-ray
  
|X-ray
 
|2.00
  
|2.00
  +
|0.176
−
|
  
 
|A
  
|A
 
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
  
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
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|X-ray
  
|X-ray
 
|2.10
  
|2.10
  +
|0.206
−
|
  
 
|A
  
|A
 
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
  
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
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|X-ray
  
|X-ray
 
|2.20
  
|2.20
  +
|0.213
−
|
  
 
|A
  
|A
 
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
  
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
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|X-ray
  
|X-ray
 
|3.10
  
|3.10
  +
|0.251
−
|
  
 
|A/B
  
|A/B
 
|[http://www.uniprot.org/blast/?about=P00439%5B118-452%5D 118-452]
  
|[http://www.uniprot.org/blast/?about=P00439%5B118-452%5D 118-452]
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|X-ray
  
|X-ray
 
|2.00
  
|2.00
  +
|0.175
−
|
  
 
|A
  
|A
 
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
  
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
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|X-ray
  
|X-ray
 
|2.11
  
|2.11
  +
|0.204
−
|
  
 
|A
  
|A
 
|[http://www.uniprot.org/blast/?about=P00439%5B104-427%5D 104-427]
  
|[http://www.uniprot.org/blast/?about=P00439%5B104-427%5D 104-427]
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|X-ray
  
|X-ray
 
|2.00
  
|2.00
  +
−
|
  
  +
|0.169
 
|A
  
|A
 
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
  
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
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|X-ray
  
|X-ray
 
|2.10
  
|2.10
  +
|0.163
−
|
  
 
|A
  
|A
 
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
  
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
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|X-ray
 
|X-ray
 
|2.15
  
|2.15
  +
|0.171
−
|
  
 
|A
  
|A
 
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
  
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]

Revision as of 13:34, 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">

Table with results from UNIProt with r-Value inserted
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.

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