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the missing residues, non-classical amino-acids, and sequence gaps have been replaced by a "X" symbol.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 ALY B 16 O - C - N ANGL. DEV. = -12.8 DEGREES REMARK 500 ALY B 16 72.60 -104.04 REMARK 500 ALY B 16 25.01 MODRES 3UVY ALY B 16 LYS N(6)-ACETYLLYSINE LINK C ALA B 15 N ALY B 16 1555 1555 1.31 LINK C ALY B 16 N ARG B 17 1555 1555 1.32 HETATM 926 OH ALY B 16 68.911 23.491 15.917 1.00 19.26 O HETATM 927 CH ALY B 16 69.117 23.369 14.728 1.00 27.06 C HETATM 928 CH3 ALY B 16 68.034 23.474 13.689 1.00 13.18 C HETATM 929 NZ ALY B 16 70.347 23.132 14.331 1.00 20.29 N HETATM 930 CE ALY B 16 71.477 22.998 15.252 1.00 18.08 C HETATM 931 CD ALY B 16 72.475 24.107 14.954 1.00 22.23 C HETATM 932 CG ALY B 16 73.692 24.034 15.849 1.00 25.64 C HETATM 933 CB ALY B 16 73.263 24.294 17.260 1.00 16.36 C HETATM 934 CA ALY B 16 74.306 24.922 18.162 1.00 21.40 C HETATM 935 N ALY B 16 73.723 24.967 19.518 1.00 24.05 N HETATM 936 C ALY B 16 74.716 26.284 17.598 1.00 29.79 C HETATM 937 O ALY B 16 73.839 27.161 17.450 1.00 28.59 O
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