From: Aditya Ranganathan (aditya.sia_at_gmail.com)
Date: Sat Aug 14 2010 - 05:57:28 CDT
Hello All,
I`m at the moment looking at starting a simulation with somatostatin which
is 14-residues long and has the following sequence:.*
Ala-Gly-Cys-Lys-Asn-Phe-Phe-Trp-Lys-Thr-Phe-Thr-Ser-Cys.*
However, the only coordinates available on PDB and structures resolved are
of synthetic constructs of somatostatin analogues which have modified
residues or nontypical residues. Is there a method by which I could change
those non-typical residues like D-TRYPTOPHAN or 3-IODO-TYROSINE or
4-[(ISOPROPYLAMINO)METHYL]PHENYLALANINE
to the ones which are present in the actual peptide.
Also, the coordinates of analogue structure in PDB does not have the Asn
residue which is present in somatostatin peptide at the 5th position between
the Lys and Phe residues.
Is there a way I could add the missing residue to the available PDB file? I
would also like to notify that the peptide forms a ring like structure or
cyclic structure between the Cys at the 3rd position and Cys at the last
position.
Please help me out with this as I need it urgently as a part of my project.
Thanks,
Srivastav Ranganathan
Junior Research Assistant and Masters Student,
IIT-Bombay, Mumbai,
India
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