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the missing residues, non-classical amino-acids, and sequence gaps have been replaced by a "X" symbol.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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This structure was solved By NMR. The PDB records below correspond to the MODEL 1.
REMARK 500 1 ALY B 16 -45.43 -172.29 REMARK 500 2 ALY B 16 -58.14 -150.04 MODRES 2KWN ALY B 16 LYS N(6)-ACETYLLYSINE LINK C ALA B 15 N ALY B 16 1555 1555 1.33 LINK C ALY B 16 N ARG B 17 1555 1555 1.33 HETATM 82 OH ALY B 16 -4.695 -4.511 1.142 1.00 0.00 O HETATM 83 CH ALY B 16 -5.519 -5.326 0.726 1.00 0.00 C HETATM 84 CH3 ALY B 16 -6.015 -5.171 -0.714 1.00 0.00 C HETATM 85 NZ ALY B 16 -6.255 -6.046 1.565 1.00 0.00 N HETATM 86 CE ALY B 16 -6.546 -5.590 2.918 1.00 0.00 C HETATM 87 CD ALY B 16 -5.832 -6.412 3.981 1.00 0.00 C HETATM 88 CG ALY B 16 -6.236 -5.974 5.383 1.00 0.00 C HETATM 89 CB ALY B 16 -5.667 -6.901 6.448 1.00 0.00 C HETATM 90 CA ALY B 16 -4.717 -6.212 7.437 1.00 0.00 C HETATM 91 N ALY B 16 -5.407 -5.150 8.165 1.00 0.00 N HETATM 92 C ALY B 16 -3.499 -5.672 6.695 1.00 0.00 C HETATM 93 O ALY B 16 -2.423 -6.270 6.743 1.00 0.00 O HETATM 94 HH31 ALY B 16 -6.489 -6.087 -1.033 1.00 0.00 H HETATM 95 HH32 ALY B 16 -6.729 -4.360 -0.759 1.00 0.00 H HETATM 96 HH33 ALY B 16 -5.179 -4.952 -1.362 1.00 0.00 H HETATM 97 HZ ALY B 16 -6.889 -6.685 1.178 1.00 0.00 H HETATM 98 HE3 ALY B 16 -6.238 -4.555 3.009 1.00 0.00 H HETATM 99 HE2 ALY B 16 -7.609 -5.660 3.085 1.00 0.00 H HETATM 100 HD3 ALY B 16 -6.087 -7.453 3.851 1.00 0.00 H HETATM 101 HD2 ALY B 16 -4.766 -6.282 3.867 1.00 0.00 H HETATM 102 HG3 ALY B 16 -5.870 -4.974 5.558 1.00 0.00 H HETATM 103 HG2 ALY B 16 -7.313 -5.982 5.453 1.00 0.00 H HETATM 104 HB3 ALY B 16 -6.492 -7.327 7.000 1.00 0.00 H HETATM 105 HB2 ALY B 16 -5.132 -7.696 5.951 1.00 0.00 H HETATM 106 HA ALY B 16 -4.383 -6.940 8.161 1.00 0.00 H HETATM 107 H ALY B 16 -5.125 -4.221 8.034 1.00 0.00 H
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