
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   43 (  172),  selected   43 , name T0320TS307_5u-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS307_5u-D2.T0320_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N     228      N     228           -
LGA    N     229      N     229           -
LGA    S     230      S     230           -
LGA    L     231      L     231           -
LGA    P     232      P     232           -
LGA    -       -      N     233           -
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    -       -      R     237           -
LGA    N     233      K     238          5.091
LGA    P     234      D     239          2.100
LGA    H     235      S     240          3.275
LGA    L     236      N     241          2.151
LGA    R     237      -       -           -
LGA    K     238      N     242          1.619
LGA    D     239      P     243          1.131
LGA    S     240      -       -           -
LGA    N     241      -       -           -
LGA    N     242      -       -           -
LGA    P     243      A     244          0.580
LGA    A     244      L     245          2.279
LGA    L     245      -       -           -
LGA    H     246      -       -           -
LGA    F     247      H     246          2.007
LGA    E     248      F     247          1.857
LGA    W     249      E     248          1.982
LGA    E     250      W     249          1.552
LGA    I     251      E     250          0.946
LGA    I     252      I     251          1.209
LGA    H     253      I     252          0.926
LGA    -       -      H     253           -
LGA    -       -      A     254           -
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    A     254      S     264          2.636
LGA    F     255      S     265          3.899
LGA    G     256      A     266          2.442
LGA    K     257      -       -           -
LGA    D     258      I     267          2.550
LGA    A     259      N     268          3.350
LGA    E     260      -       -           -
LGA    G     261      -       -           -
LGA    E     262      T     269          1.845
LGA    R     263      S     270          3.156
LGA    S     264      P     271          2.505
LGA    S     265      -       -           -
LGA    A     266      I     272          4.615
LGA    I     267      S     273          3.429
LGA    N     268      V     274           #
LGA    T     269      V     275           -
LGA    S     270      D     276           #
LGA    -       -      K     277           -
LGA    -       -      E     278           -
LGA    -       -      R     279           -
LGA    -       -      F     280           -
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    -       -      Y     283           -
LGA    -       -      H     284           -
LGA    -       -      D     285           -
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      E     299           -
LGA    -       -      R     300           -
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    -       -      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43   73    5.0     25    2.61     4.00     24.925     0.922

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.951987 * X  +   0.260688 * Y  +   0.160505 * Z  + -20.346634
  Y_new =  -0.290322 * X  +  -0.935111 * Y  +  -0.203176 * Z  +  26.918661
  Z_new =   0.097124 * X  +  -0.240019 * Y  +   0.965897 * Z  + -53.145653 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.243560    2.898033  [ DEG:   -13.9550    166.0450 ]
  Theta =  -0.097278   -3.044315  [ DEG:    -5.5736   -174.4264 ]
  Phi   =  -2.845588    0.296005  [ DEG:  -163.0402     16.9598 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0320TS307_5u-D2                              
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS307_5u-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43   73   5.0   25   2.61    4.00  24.925
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS307_5u-D2
PFRMAT   TS
TARGET   T0320
MODEL    5  UNREFINED
PARENT   1wy5_A
ATOM     1   N   ASN   228       5.686  12.134 -16.904  1.00                    
ATOM     1   CA  ASN   228       6.606  11.102 -16.422  1.00                    
ATOM     1   C   ASN   228       7.355  11.444 -15.141  1.00                    
ATOM     1   O   ASN   228       7.933  10.563 -14.507  1.00                    
ATOM     1   N   ASN   229       7.365  12.720 -14.779  1.00                    
ATOM     1   CA  ASN   229       8.032  13.198 -13.572  1.00                    
ATOM     1   C   ASN   229       7.485  12.532 -12.305  1.00                    
ATOM     1   O   ASN   229       8.223  12.281 -11.350  1.00                    
ATOM     1   N   SER   230       6.190  12.256 -12.299  1.00                    
ATOM     1   CA  SER   230       5.549  11.621 -11.161  1.00                    
ATOM     1   C   SER   230       6.092  10.227 -10.906  1.00                    
ATOM     1   O   SER   230       5.992   9.713  -9.789  1.00                    
ATOM     1   N   LEU   231       6.675   9.610 -11.928  1.00                    
ATOM     1   CA  LEU   231       7.189   8.260 -11.772  1.00                    
ATOM     1   C   LEU   231       8.693   8.164 -11.554  1.00                    
ATOM     1   O   LEU   231       9.276   7.084 -11.644  1.00                    
ATOM     1   N   PRO   232       9.320   9.295 -11.257  1.00                    
ATOM     1   CA  PRO   232      10.749   9.302 -10.987  1.00                    
ATOM     1   C   PRO   232      10.963   9.678  -9.529  1.00                    
ATOM     1   O   PRO   232      12.063   9.528  -8.998  1.00                    
ATOM     1   N   ASN   233       9.904  10.182  -8.895  1.00                    
ATOM     1   CA  ASN   233       9.968  10.625  -7.507  1.00                    
ATOM     1   C   ASN   233      10.677   9.595  -6.639  1.00                    
ATOM     1   O   ASN   233      10.363   8.410  -6.696  1.00                    
ATOM     1   N   PRO   234      11.638  10.047  -5.840  1.00                    
ATOM     1   CA  PRO   234      12.370   9.135  -4.969  1.00                    
ATOM     1   C   PRO   234      11.485   8.671  -3.824  1.00                    
ATOM     1   O   PRO   234      10.503   9.332  -3.467  1.00                    
ATOM     1   N   HIS   235      11.838   7.530  -3.247  1.00                    
ATOM     1   CA  HIS   235      11.085   6.972  -2.135  1.00                    
ATOM     1   C   HIS   235      11.021   7.944  -0.951  1.00                    
ATOM     1   O   HIS   235       9.957   8.133  -0.358  1.00                    
ATOM     1   N   LEU   236      12.155   8.569  -0.586  1.00                    
ATOM     1   CA  LEU   236      12.145   9.514   0.534  1.00                    
ATOM     1   C   LEU   236      11.164  10.665   0.353  1.00                    
ATOM     1   O   LEU   236      10.481  11.056   1.295  1.00                    
ATOM     1   N   ARG   237      11.100  11.209  -0.855  1.00                    
ATOM     1   CA  ARG   237      10.211  12.325  -1.139  1.00                    
ATOM     1   C   ARG   237       8.750  11.887  -1.154  1.00                    
ATOM     1   O   ARG   237       7.865  12.655  -0.767  1.00                    
ATOM     1   N   LYS   238       8.489  10.659  -1.589  1.00                    
ATOM     1   CA  LYS   238       7.119  10.169  -1.593  1.00                    
ATOM     1   C   LYS   238       6.652   9.964  -0.157  1.00                    
ATOM     1   O   LYS   238       5.497  10.221   0.166  1.00                    
ATOM     1   N   ASP   239       7.552   9.510   0.709  1.00                    
ATOM     1   CA  ASP   239       7.191   9.302   2.105  1.00                    
ATOM     1   C   ASP   239       6.784  10.635   2.713  1.00                    
ATOM     1   O   ASP   239       5.789  10.739   3.427  1.00                    
ATOM     1   N   SER   240       7.564  11.662   2.422  1.00                    
ATOM     1   CA  SER   240       7.289  12.981   2.955  1.00                    
ATOM     1   C   SER   240       6.053  13.620   2.344  1.00                    
ATOM     1   O   SER   240       5.268  14.256   3.037  1.00                    
ATOM     1   N   ASN   241       5.869  13.414   1.046  1.00                    
ATOM     1   CA  ASN   241       4.743  13.982   0.335  1.00                    
ATOM     1   C   ASN   241       3.389  13.361   0.688  1.00                    
ATOM     1   O   ASN   241       2.425  14.081   0.940  1.00                    
ATOM     1   N   ASN   242       3.329  12.034   0.732  1.00                    
ATOM     1   CA  ASN   242       2.078  11.329   0.989  1.00                    
ATOM     1   C   ASN   242       1.856  10.777   2.382  1.00                    
ATOM     1   O   ASN   242       0.791  10.220   2.656  1.00                    
ATOM     1   N   PRO   243       2.841  10.918   3.262  1.00                    
ATOM     1   CA  PRO   243       2.697  10.405   4.618  1.00                    
ATOM     1   C   PRO   243       3.028  11.426   5.685  1.00                    
ATOM     1   O   PRO   243       2.225  11.657   6.592  1.00                    
ATOM     1   N   ALA   244       4.202  12.043   5.593  1.00                    
ATOM     1   CA  ALA   244       4.578  13.022   6.596  1.00                    
ATOM     1   C   ALA   244       3.800  14.338   6.506  1.00                    
ATOM     1   O   ALA   244       3.177  14.751   7.487  1.00                    
ATOM     1   N   LEU   245       3.831  14.993   5.345  1.00                    
ATOM     1   CA  LEU   245       3.120  16.259   5.187  1.00                    
ATOM     1   C   LEU   245       1.627  16.134   5.551  1.00                    
ATOM     1   O   LEU   245       1.090  16.983   6.255  1.00                    
ATOM     1   N   HIS   246       0.939  15.074   5.088  1.00                    
ATOM     1   CA  HIS   246      -0.482  14.958   5.452  1.00                    
ATOM     1   C   HIS   246      -0.663  14.940   6.979  1.00                    
ATOM     1   O   HIS   246      -1.607  15.539   7.503  1.00                    
ATOM     1   N   PHE   247       0.243  14.260   7.689  1.00                    
ATOM     1   CA  PHE   247       0.172  14.210   9.150  1.00                    
ATOM     1   C   PHE   247       0.427  15.580   9.768  1.00                    
ATOM     1   O   PHE   247      -0.242  15.970  10.722  1.00                    
ATOM     1   N   GLU   248       1.406  16.304   9.231  1.00                    
ATOM     1   CA  GLU   248       1.733  17.615   9.749  1.00                    
ATOM     1   C   GLU   248       0.583  18.576   9.523  1.00                    
ATOM     1   O   GLU   248       0.318  19.443  10.356  1.00                    
ATOM     1   N   TRP   249      -0.099  18.419   8.393  1.00                    
ATOM     1   CA  TRP   249      -1.219  19.289   8.054  1.00                    
ATOM     1   C   TRP   249      -2.441  18.999   8.912  1.00                    
ATOM     1   O   TRP   249      -3.373  19.795   8.966  1.00                    
ATOM     1   N   GLU   250      -2.430  17.861   9.594  1.00                    
ATOM     1   CA  GLU   250      -3.540  17.512  10.467  1.00                    
ATOM     1   C   GLU   250      -3.331  18.282  11.772  1.00                    
ATOM     1   O   GLU   250      -4.267  18.500  12.535  1.00                    
ATOM     1   N   ILE   251      -2.086  18.686  12.016  1.00                    
ATOM     1   CA  ILE   251      -1.728  19.471  13.187  1.00                    
ATOM     1   C   ILE   251      -1.950  20.947  12.829  1.00                    
ATOM     1   O   ILE   251      -2.588  21.683  13.576  1.00                    
ATOM     1   N   ILE   252      -1.407  21.364  11.687  1.00                    
ATOM     1   CA  ILE   252      -1.557  22.727  11.201  1.00                    
ATOM     1   C   ILE   252      -2.074  22.732   9.761  1.00                    
ATOM     1   O   ILE   252      -1.357  22.411   8.808  1.00                    
ATOM     1   N   HIS   253      -3.335  23.108   9.627  1.00                    
ATOM     1   CA  HIS   253      -4.037  23.182   8.354  1.00                    
ATOM     1   C   HIS   253      -3.351  24.067   7.299  1.00                    
ATOM     1   O   HIS   253      -3.419  23.789   6.102  1.00                    
ATOM     1   N   ALA   254      -2.690  25.131   7.741  1.00                    
ATOM     1   CA  ALA   254      -2.024  26.033   6.809  1.00                    
ATOM     1   C   ALA   254      -0.507  25.906   6.891  1.00                    
ATOM     1   O   ALA   254       0.200  26.913   6.972  1.00                    
ATOM     1   N   PHE   255      -0.017  24.668   6.859  1.00                    
ATOM     1   CA  PHE   255       1.413  24.388   6.946  1.00                    
ATOM     1   C   PHE   255       2.242  25.190   5.945  1.00                    
ATOM     1   O   PHE   255       3.265  25.768   6.315  1.00                    
ATOM     1   N   GLY   256       1.797  25.235   4.685  1.00                    
ATOM     1   CA  GLY   256       2.530  25.960   3.640  1.00                    
ATOM     1   C   GLY   256       2.676  27.454   3.924  1.00                    
ATOM     1   O   GLY   256       3.759  28.014   3.761  1.00                    
ATOM     1   N   LYS   257       1.598  28.102   4.351  1.00                    
ATOM     1   CA  LYS   257       1.649  29.530   4.644  1.00                    
ATOM     1   C   LYS   257       2.600  29.789   5.801  1.00                    
ATOM     1   O   LYS   257       3.366  30.752   5.799  1.00                    
ATOM     1   N   ASP   258       2.543  28.915   6.790  1.00                    
ATOM     1   CA  ASP   258       3.399  29.024   7.952  1.00                    
ATOM     1   C   ASP   258       4.875  28.786   7.591  1.00                    
ATOM     1   O   ASP   258       5.769  29.536   8.003  1.00                    
ATOM     1   N   ALA   259       5.112  27.739   6.811  1.00                    
ATOM     1   CA  ALA   259       6.442  27.381   6.365  1.00                    
ATOM     1   C   ALA   259       7.103  28.540   5.600  1.00                    
ATOM     1   O   ALA   259       8.275  28.859   5.837  1.00                    
ATOM     1   N   GLU   260       6.356  29.166   4.687  1.00                    
ATOM     1   CA  GLU   260       6.891  30.285   3.910  1.00                    
ATOM     1   C   GLU   260       7.420  31.398   4.807  1.00                    
ATOM     1   O   GLU   260       8.434  32.019   4.498  1.00                    
ATOM     1   N   GLY   261       6.739  31.661   5.919  1.00                    
ATOM     1   CA  GLY   261       7.198  32.706   6.824  1.00                    
ATOM     1   C   GLY   261       8.539  32.324   7.445  1.00                    
ATOM     1   O   GLY   261       9.405  33.180   7.635  1.00                    
ATOM     1   N   GLU   262       8.708  31.039   7.750  1.00                    
ATOM     1   CA  GLU   262       9.954  30.541   8.327  1.00                    
ATOM     1   C   GLU   262      11.062  30.780   7.308  1.00                    
ATOM     1   O   GLU   262      12.114  31.323   7.637  1.00                    
ATOM     1   N   ARG   263      10.814  30.375   6.066  1.00                    
ATOM     1   CA  ARG   263      11.794  30.553   5.001  1.00                    
ATOM     1   C   ARG   263      12.242  32.013   4.915  1.00                    
ATOM     1   O   ARG   263      13.435  32.302   4.862  1.00                    
ATOM     1   N   SER   264      11.289  32.937   4.918  1.00                    
ATOM     1   CA  SER   264      11.637  34.348   4.845  1.00                    
ATOM     1   C   SER   264      12.446  34.794   6.064  1.00                    
ATOM     1   O   SER   264      13.385  35.581   5.939  1.00                    
ATOM     1   N   SER   265      12.095  34.303   7.245  1.00                    
ATOM     1   CA  SER   265      12.866  34.679   8.418  1.00                    
ATOM     1   C   SER   265      14.281  34.093   8.263  1.00                    
ATOM     1   O   SER   265      15.283  34.804   8.420  1.00                    
ATOM     1   N   ALA   266      14.359  32.804   7.931  1.00                    
ATOM     1   CA  ALA   266      15.644  32.138   7.760  1.00                    
ATOM     1   C   ALA   266      16.531  32.820   6.718  1.00                    
ATOM     1   O   ALA   266      17.719  33.030   6.963  1.00                    
ATOM     1   N   ILE   267      15.967  33.183   5.568  1.00                    
ATOM     1   CA  ILE   267      16.760  33.840   4.530  1.00                    
ATOM     1   C   ILE   267      17.353  35.188   4.940  1.00                    
ATOM     1   O   ILE   267      18.448  35.529   4.504  1.00                    
ATOM     1   N   ASN   268      16.651  35.957   5.772  1.00                    
ATOM     1   CA  ASN   268      17.191  37.241   6.213  1.00                    
ATOM     1   C   ASN   268      18.304  36.964   7.220  1.00                    
ATOM     1   O   ASN   268      19.348  37.616   7.211  1.00                    
ATOM     1   N   THR   269      18.085  35.974   8.081  1.00                    
ATOM     1   CA  THR   269      19.089  35.617   9.076  1.00                    
ATOM     1   C   THR   269      20.347  35.060   8.398  1.00                    
ATOM     1   O   THR   269      21.465  35.330   8.836  1.00                    
ATOM     1   N   SER   270      20.170  34.295   7.322  1.00                    
ATOM     1   CA  SER   270      21.315  33.734   6.607  1.00                    
ATOM     1   C   SER   270      22.084  34.864   5.930  1.00                    
ATOM     1   O   SER   270      23.310  34.935   6.003  1.00                    
TER
END
