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Tuesday 12 April 2011

3QXE- the new NHase pdb file- from Pseudomonas putida

I thought I'd have a look to see how different the new pdb file was from those already in the public domain.
First of all a ClustalW alignment of the alpha chains shows that it has a score of 52 with 1V29 and a score of 54 with 1UGP. (For reference, 1V29 and 1UGP have a score of 59 between them). The numbers might not be completely robust because I note that the modified cysteines are not dealt with the same in the three amino acid sequences. The central portions of the sequence are very similar, with most of the diversity at the ends (see below: 1V29 then 1UGP and finally 3QXE)
Using DeepView's RMS measure of 3D similarity after an Iterative Magic Fit of  the new pdb with the files for 1V29 and 1UGP enzymes you get two numbers of approximately 1-1.05 (for reference between 1V29 and 1UGP the value is 1.15). This all suggests that this new file describes a new distinct structural arrangement.

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