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

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(→‎Finding the right structure)
(→‎Finding the right structure)
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== Finding the right structure ==
  
== Finding the right structure ==
 
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, if you like to have a look at all the possibilities, or try what we did on another similar example feel free to browse [[Structures for P00439 in PDB|all our results]]
 +
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">
  +
<center><caption>Table with results from UNIProt with r-Value inserted</caption></center>
  +
{| align="center"
  +
!|Entry
  +
!|Method
  +
!|Resolution (Å)
  +
!|r-Value
  +
!|Chain
  +
!|Positions
  +
!|PDBsum
  +
|-
  +
|[http://www.ebi.ac.uk/pdbe-srv/view/entry/1DMW 1DMW]
  +
|X-ray
  +
|2.00
  +
|
  +
|A
  +
|[http://www.uniprot.org/blast/?about=P00439%5B118-424%5D 118-424]
  +
|[[http://www.ebi.ac.uk/pdbsum/1DMW »]]
  +
|-
  +
|[http://www.ebi.ac.uk/pdbe-srv/view/entry/1J8T 1J8T]
  +
|X-ray
  +
|1.70
  +
|
  +
|A
  +
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
  +
|[[http://www.ebi.ac.uk/pdbsum/1J8T »]]
  +
|-
  +
|[http://www.ebi.ac.uk/pdbe-srv/view/entry/1J8U 1J8U]
  +
|X-ray
  +
|1.50
  +
|
  +
|A
  +
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
  +
|[[http://www.ebi.ac.uk/pdbsum/1J8U »]]
  +
|-
  +
|[http://www.ebi.ac.uk/pdbe-srv/view/entry/1KW0 1KW0]
  +
|X-ray
  +
|2.50
  +
|
  +
|A
  +
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
  +
|[[http://www.ebi.ac.uk/pdbsum/1KW0 »]]
  +
|-
  +
|[http://www.ebi.ac.uk/pdbe-srv/view/entry/1LRM 1LRM]
  +
|X-ray
  +
|2.10
  +
|
  +
|A
  +
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
  +
|[[http://www.ebi.ac.uk/pdbsum/1LRM »]]
  +
|-
  +
|[http://www.ebi.ac.uk/pdbe-srv/view/entry/1MMK 1MMK]
  +
|X-ray
  +
|2.00
  +
|
  +
|A
  +
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
  +
|[[http://www.ebi.ac.uk/pdbsum/1MMK »]]
  +
|-
  +
|[http://www.ebi.ac.uk/pdbe-srv/view/entry/1MMT 1MMT]
  +
|X-ray
  +
|2.00
  +
|
  +
|A
  +
|[http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427]
  +
|[[http://www.ebi.ac.uk/pdbsum/1MMT »]]
  +
|-
  +
|[http://www.ebi.ac.uk/pdbe-srv/view/entry/1PAH 1PAH]
  +
|X-ray
  +
|2.00
  +
|
  +
|A
  +
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
  +
|[[http://www.ebi.ac.uk/pdbsum/1PAH »]]
  +
|-
  +
|[http://www.ebi.ac.uk/pdbe-srv/view/entry/1TDW 1TDW]
  +
|X-ray
  +
|2.10
  +
|
  +
|A
  +
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
  +
|[[http://www.ebi.ac.uk/pdbsum/1TDW »]]
  +
|-
  +
|[http://www.ebi.ac.uk/pdbe-srv/view/entry/1TG2 1TG2]
  +
|X-ray
  +
|2.20
  +
|
  +
|A
  +
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
  +
|[[http://www.ebi.ac.uk/pdbsum/1TG2 »]]
  +
|-
  +
|[http://www.ebi.ac.uk/pdbe-srv/view/entry/2PAH 2PAH]
  +
|X-ray
  +
|3.10
  +
|
  +
|A/B
  +
|[http://www.uniprot.org/blast/?about=P00439%5B118-452%5D 118-452]
  +
|[[http://www.ebi.ac.uk/pdbsum/2PAH »]]
  +
|-
  +
|[http://www.ebi.ac.uk/pdbe-srv/view/entry/3PAH 3PAH]
  +
|X-ray
  +
|2.00
  +
|
  +
|A
  +
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
  +
|[[http://www.ebi.ac.uk/pdbsum/3PAH »]]
  +
|-
  +
|[http://www.ebi.ac.uk/pdbe-srv/view/entry/4ANP 4ANP]
  +
|X-ray
  +
|2.11
  +
|
  +
|A
  +
|[http://www.uniprot.org/blast/?about=P00439%5B104-427%5D 104-427]
  +
|[[http://www.ebi.ac.uk/pdbsum/4ANP »]]
  +
|-
  +
|[http://www.ebi.ac.uk/pdbe-srv/view/entry/4PAH 4PAH]
  +
|X-ray
  +
|2.00
  +
|
  +
|A
  +
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
  +
|[[http://www.ebi.ac.uk/pdbsum/4PAH »]]
  +
|-
  +
|[http://www.ebi.ac.uk/pdbe-srv/view/entry/5PAH 5PAH]
  +
|X-ray
  +
|2.10
  +
|
  +
|A
  +
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
  +
|[[http://www.ebi.ac.uk/pdbsum/5PAH »]]
  +
|-
  +
|[http://www.ebi.ac.uk/pdbe-srv/view/entry/6PAH 6PAH]
  +
|X-ray
  +
|2.15
  +
|
  +
|A
  +
|[http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424]
  +
|[[http://www.ebi.ac.uk/pdbsum/6PAH »]]
  +
|-
  +
|}
  +
</figtable>
  +
In <xr id="uniprotresult"/> there are all results according to which we selected 1J8U to be our reference for this weeks task.

Revision as of 13:28, 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. 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">

Table with results from UNIProt with r-Value inserted
Entry Method Resolution (Å) r-Value Chain Positions PDBsum
1DMW X-ray 2.00 A 118-424 [»]
1J8T X-ray 1.70 A 103-427 [»]
1J8U X-ray 1.50 A 103-427 [»]
1KW0 X-ray 2.50 A 103-427 [»]
1LRM X-ray 2.10 A 103-427 [»]
1MMK X-ray 2.00 A 103-427 [»]
1MMT X-ray 2.00 A 103-427 [»]
1PAH X-ray 2.00 A 117-424 [»]
1TDW X-ray 2.10 A 117-424 [»]
1TG2 X-ray 2.20 A 117-424 [»]
2PAH X-ray 3.10 A/B 118-452 [»]
3PAH X-ray 2.00 A 117-424 [»]
4ANP X-ray 2.11 A 104-427 [»]
4PAH X-ray 2.00 A 117-424 [»]
5PAH X-ray 2.10 A 117-424 [»]
6PAH X-ray 2.15 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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