Modeller
If you want to use this structure as a template for modelisation with Modeller, you can use the following sequence to build the alignment file "*.ali".
To avoid the classical Modeller error :
'Number of residues in the alignment and pdb files are different'(see FAQ n°17),
the missing residues, non-classical amino-acids, and sequence gaps have been replaced by a "X" symbol.
1) align this sequence with your sequence to modelised;
2) replace the "X" by "-" in the obtained alignement, then build your "*.ali" file;
3) use Modeller to make your models;
4) And finally use the following information found in the PDB to add this PTM in your models (see FAQ n°8 & 9 and this archive of Modeller usage).
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REMARK 500 M3L C 20 -151.96 178.20
MODRES 2QQS M3L C 20 LYS N-TRIMETHYLLYSINE
LINK C ARG C 19 N M3L C 20 1555 1555 1.33
LINK C M3L C 20 N VAL C 21 1555 1555 1.45
HETATM 1780 N M3L C 20 12.253 1.127 29.707 1.00 46.50 N
HETATM 1781 CA M3L C 20 13.123 0.116 30.345 1.00 46.81 C
HETATM 1782 CB M3L C 20 13.618 0.512 31.752 1.00 46.87 C
HETATM 1783 CG M3L C 20 14.523 1.790 31.810 1.00 46.51 C
HETATM 1784 CD M3L C 20 15.561 1.576 32.920 1.00 46.50 C
HETATM 1785 CE M3L C 20 14.898 1.149 34.246 1.00 47.62 C
HETATM 1786 NZ M3L C 20 15.256 1.997 35.419 1.00 49.15 N
HETATM 1787 C M3L C 20 14.356 -0.237 29.492 1.00 47.10 C
HETATM 1788 O M3L C 20 15.046 0.697 28.916 1.00 47.91 O
HETATM 1789 CM1 M3L C 20 14.339 1.665 36.537 1.00 47.87 C
HETATM 1790 CM2 M3L C 20 16.644 1.709 35.845 1.00 49.76 C
HETATM 1791 CM3 M3L C 20 15.201 3.453 35.116 1.00 48.23 C
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