[modeller_usage] 2 BLK in one model

[Isaure Chauvot de Beauchêne <>]

Hi,

I'm trying to model a complex of 3 components: a peptide including 2  
phosphotyrosines, and 2 signal protein recognizing each one  
phosphotyrosine.
I have 2 templates, one for each complex protein-phosphopeptide. I've  
put each PTR as BLK. But one of the PTR is changed in ASP in my  
results, because Modeller change the alignment I gave in my .ali file.

This is the alignment file:

> P1;2iuh        #Pi3k
structureX:2iuh:4:A:208:B::::
--------------------------------------------------------------------------------
--------------------------NMSLQNAEWYWGDISREEVNEKLRDTADGTFLVRDASTKMHGDYTLTLRKGGNN
KLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKLDVKLLYPVSKYQQDQVVKE-/
TNE.MDMK-------------*

> P1;2pld        #PLC
structureX:2pld:1:A:12:B::::
GSPGIHESKEWYHASLTRAQAEHMLMRVPRDGAFLVRKRNEPNSYAISFRAEGKIKHCRVQQEGQTVMLGNSEFDSLVDL
ISYYEKHPLYRKMKLRYPINEENSS/-------------------------------------------------------
--------------------------------------------------------------/
---------DNDYIIPLPDPK*

> P1;comp
sequence:comp:1:A:21:C::::
GSPGIHESKEWYHASLTRAQAEHMLMRVPRDGAFLVRKRNEPNSYAISFRAEGKIKHCRVQQEGQTVMLGNSEFDSLVDL
ISYYEKHPLYRKMKLRYPINEENSS/NMSLQNAEWYWGDISREEVNEKLRDTADGTFLVRDASTKMHGDYTLTLRKGGNN
KLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKLDVKLLYPVSKYQQDQVVKED/
TNE.MDMKPGVSYVVPTKADK*

and this is part of the .out:

read_te_291E> Sequence difference between alignment and  pdb :
                  x  (mismatch at alignment position    120)
 Alignment   ETNE.MDMK
          PDB   ETNEMDMK
        Match   *****
  Alignment residue type   11 (M, MET) does not match pdb
  residue type    3 (D, ASP),
  for align code 2iuh (atom file 2iuh), pdb residue number "206", chain "B"


This is the PTR of the template 2iuh:
ATOM    967  CD  GLU B 203      28.500  18.086  19.085  1.00 23.93           C
ATOM    968  OE1 GLU B 203      28.474  16.841  18.975  1.00 25.60           O
ATOM    969  OE2 GLU B 203      29.534  18.753  18.901  1.00 25.56      
      O1-
HETATM  970  N   BLK B 204      23.987  20.311  19.503  1.00 17.56           N
HETATM  971  CA  BLK B 204      23.170  20.645  18.345  1.00 17.48           C
HETATM  972  C   BLK B 204      23.958  20.440  17.054  1.00 17.87           C
HETATM  973  O   BLK B 204      25.071  20.949  16.905  1.00 17.97           O
HETATM  974  CB  BLK B 204      22.668  22.083  18.435  1.00 16.51           C
HETATM  975  CG  BLK B 204      21.236  22.165  18.925  1.00 16.28           C
HETATM  976  CD1 BLK B 204      20.236  21.731  18.070  1.00 16.08           C
HETATM  977  CD2 BLK B 204      20.937  22.626  20.204  1.00 15.99           C
HETATM  978  CE1 BLK B 204      18.914  21.746  18.468  1.00 15.70           C
HETATM  979  CE2 BLK B 204      19.616  22.637  20.615  1.00 15.90           C
HETATM  980  CZ  BLK B 204      18.643  22.197  19.729  1.00 16.36           C
HETATM  981  OH  BLK B 204      17.254  22.157  20.018  1.00 16.93           O
HETATM  982  P   BLK B 204      16.513  22.838  21.260  1.00 16.40           P
HETATM  983  O1P BLK B 204      15.064  22.662  21.118  1.00 15.57           O
HETATM  984  O2P BLK B 204      16.982  22.261  22.527  1.00 16.50      
      O1-
HETATM  985  O3P BLK B 204      16.829  24.260  21.166  1.00 17.35           O
ATOM    986  N   MET B 205      23.429  19.583  16.187  1.00 17.64           N
ATOM    987  CA  MET B 205      24.111  19.203  14.953  1.00 17.33           C
ATOM    988  C   MET B 205      23.824  20.152  13.795  1.00 17.59


Do you have an idea of why Modeller switch the PTR of my template?
Many thanks in advance,

Isaure



--
Isaure Chauvot de Beauchêne
Ph.D student
Team: "Bioinformatics, Modelisation and Molecular Dynamics" (BiMoDyM)
Dir Luba Tchertanov,LBPA-CNRS, ENS-Cachan
61 Av du Pr Wilson, 94230 Cachan, FRANCE