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the missing residues, non-classical amino-acids, and sequence gaps have been replaced by a "X" symbol.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 D 20 95.42 83.90
MODRES 2QQS M3L D 20 LYS N-TRIMETHYLLYSINE
LINK C ARG D 19 N M3L D 20 1555 1555 1.34
LINK C M3L D 20 N VAL D 21 1555 1555 1.34
HETATM 1832 N M3L D 20 12.439 -15.255 8.901 1.00 38.64 N
HETATM 1833 CA M3L D 20 10.963 -15.107 8.961 1.00 38.35 C
HETATM 1834 CB M3L D 20 10.157 -15.962 9.938 1.00 38.07 C
HETATM 1835 CG M3L D 20 8.792 -15.298 10.115 1.00 33.91 C
HETATM 1836 CD M3L D 20 8.300 -15.270 11.546 1.00 29.87 C
HETATM 1837 CE M3L D 20 7.178 -16.293 11.752 1.00 27.06 C
HETATM 1838 NZ M3L D 20 6.090 -15.863 12.657 1.00 24.00 N
HETATM 1839 C M3L D 20 10.236 -14.975 7.644 1.00 39.31 C
HETATM 1840 O M3L D 20 10.138 -13.863 7.126 1.00 39.37 O
HETATM 1841 CM1 M3L D 20 5.684 -14.473 12.450 1.00 23.41 C
HETATM 1842 CM2 M3L D 20 4.948 -16.713 12.364 1.00 24.75 C
HETATM 1843 CM3 M3L D 20 6.425 -16.069 14.061 1.00 23.86 C
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