Pyridoxal Phosphatase Methods: Difference between revisions
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'''PDBsum''' <BR> | '''PDBsum''' <BR> | ||
From the EBI website (http://www.ebi.ac.uk/), | From the EBI website (http://www.ebi.ac.uk/), the PDBsum structural database was accessed to obtain the secondary structures, as well as information (i.e. topology diagram, cleft analysis) pertaining to the secondary structures of both 2cfsA and 2oycA. | ||
Function | Function | ||
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Revision as of 15:52, 21 May 2008
Evolution
Structure
Protein Data Bank (PDB)
The structure of 2cfsA was obtained from the PDB. A search on the database using Pyridoxal Phosphatase's PDB ID (2cfsA) did not yield any results. A search using the PDB ID "2cfs" was successful. The crystal structure of Pyridoxal Phosphatase was obtained from the "Images and Visualization" section located on the right side of website.
http://www.rcsb.org/pdb/explore/explore.do?structureId=2cfs
The PDB file of Pyridoxal Phosphatase was saved for further use.
DALI
A search was carried out using the PDB file (obtained from the previous step) of Pyridoxal Phosphatase. The results were generated and returned via e-mail. Due its similarity to 2cfsA, 2oycA - which was at the top of the list of hits generated by the DALI server, was structurally superimposed against 2cfsA using the PyMOL software.
PDBsum
From the EBI website (http://www.ebi.ac.uk/), the PDBsum structural database was accessed to obtain the secondary structures, as well as information (i.e. topology diagram, cleft analysis) pertaining to the secondary structures of both 2cfsA and 2oycA.
Function
