
#######################################################
#                                                     #
#                        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    9 (   86),  selected    9 , name T0372TS277_3-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS277_3-D1.T0372_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    K     290      R      25          2.136
LGA    Y     291      N      26          1.150
LGA    -       -      C      27           -
LGA    M     292      D      28          3.194
LGA    A     293      L      29          2.780
LGA    C     294      S      30          0.721
LGA    L     295      F      31          2.154
LGA    K     296      S      32          2.454
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    D     297      S      36          1.208
LGA    H     298      W      37          2.283
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    -       -      E      82           -
LGA    -       -      D      83           -
LGA    -       -      A      84           -
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    -       -      F      91           -
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    9  126    5.0      9    2.15     0.00      5.969     0.400

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.869282 * X  +   0.250286 * Y  +  -0.426269 * Z  +  10.531867
  Y_new =  -0.184944 * X  +  -0.635035 * Y  +  -0.750017 * Z  + 100.648445
  Z_new =  -0.458415 * X  +   0.730813 * Y  +  -0.505735 * Z  +  14.987574 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.176145   -0.965448  [ DEG:   124.6839    -55.3161 ]
  Theta =   0.476211    2.665381  [ DEG:    27.2849    152.7151 ]
  Phi   =  -0.209630    2.931963  [ DEG:   -12.0109    167.9891 ]
 
# 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: T0372TS277_3-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS277_3-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    9  126   5.0    9   2.15    0.00   5.969
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS277_3-D1
PFRMAT TS 
TARGET T0372
MODEL 3
PARENT 1YR0_A
ATOM   2945  H   LYS   290      30.161  49.868  16.796  1.00  0.00                              
ATOM   2947  N   LYS   290      29.628  50.174  16.072  1.00  0.00                              
ATOM   2949  CA  LYS   290      30.227  51.073  15.088  1.00  0.00                              
ATOM   2951  CB  LYS   290      31.271  51.976  15.755  1.00  0.00                              
ATOM   2953  C   LYS   290      30.887  50.282  13.961  1.00  0.00                              
ATOM   2955  O   LYS   290      31.290  49.132  14.156  1.00  0.00                              
ATOM   2957  CG  LYS   290      30.695  53.012  16.711  1.00  0.00                              
ATOM   2959  CD  LYS   290      31.796  53.864  17.333  1.00  0.00                              
ATOM   2961  CE  LYS   290      31.230  54.961  18.225  1.00  0.00                              
ATOM   2963  NZ  LYS   290      32.310  55.791  18.834  1.00  0.00                              
ATOM   2965  H   TYR   291      30.699  51.777  12.685  1.00  0.00                              
ATOM   2967  N   TYR   291      31.025  50.897  12.790  1.00  0.00                              
ATOM   2969  CA  TYR   291      31.634  50.226  11.649  1.00  0.00                              
ATOM   2971  CB  TYR   291      30.678  50.226  10.458  1.00  0.00                              
ATOM   2973  C   TYR   291      32.927  50.896  11.218  1.00  0.00                              
ATOM   2975  O   TYR   291      33.025  52.125  11.215  1.00  0.00                              
ATOM   2977  CG  TYR   291      31.256  49.548   9.240  1.00  0.00                              
ATOM   2979  CD1 TYR   291      31.457  48.170   9.226  1.00  0.00                              
ATOM   2981  CE1 TYR   291      31.940  47.526   8.091  1.00  0.00                              
ATOM   2983  CZ  TYR   291      32.195  48.263   6.947  1.00  0.00                              
ATOM   2985  CD2 TYR   291      31.598  50.276   8.102  1.00  0.00                              
ATOM   2987  CE2 TYR   291      32.048  49.639   6.951  1.00  0.00                              
ATOM   2989  OH  TYR   291      32.650  47.627   5.812  1.00  0.00                              
ATOM   2991  H   MET   292      33.745  49.154  10.809  1.00  0.00                              
ATOM   2993  N   MET   292      33.894  50.088  10.795  1.00  0.00                              
ATOM   2995  CA  MET   292      35.181  50.599  10.341  1.00  0.00                              
ATOM   2997  CB  MET   292      35.132  50.951   8.853  1.00  0.00                              
ATOM   2999  C   MET   292      35.583  51.831  11.135  1.00  0.00                              
ATOM   3001  O   MET   292      35.717  52.920  10.573  1.00  0.00                              
ATOM   3003  CG  MET   292      35.221  49.743   7.935  1.00  0.00                              
ATOM   3005  SD  MET   292      36.540  48.601   8.407  1.00  0.00                              
ATOM   3007  CE  MET   292      35.590  47.284   9.150  1.00  0.00                              
ATOM   3009  H   ALA   293      35.715  50.820  12.818  1.00  0.00                              
ATOM   3011  N   ALA   293      35.840  51.661  12.431  1.00  0.00                              
ATOM   3013  CA  ALA   293      36.301  52.765  13.271  1.00  0.00                              
ATOM   3015  CB  ALA   293      35.400  52.917  14.493  1.00  0.00                              
ATOM   3017  C   ALA   293      37.750  52.562  13.710  1.00  0.00                              
ATOM   3019  O   ALA   293      38.488  53.531  13.905  1.00  0.00                              
ATOM   3021  H   CYS   294      37.591  50.608  13.611  1.00  0.00                              
ATOM   3023  N   CYS   294      38.167  51.305  13.834  1.00  0.00                              
ATOM   3025  CA  CYS   294      39.519  50.993  14.282  1.00  0.00                              
ATOM   3027  CB  CYS   294      39.488  50.376  15.684  1.00  0.00                              
ATOM   3029  C   CYS   294      40.206  50.036  13.317  1.00  0.00                              
ATOM   3031  O   CYS   294      39.618  49.033  12.905  1.00  0.00                              
ATOM   3033  SG  CYS   294      38.795  51.469  16.949  1.00  0.00                              
ATOM   3035  H   LEU   295      41.843  51.130  13.302  1.00  0.00                              
ATOM   3037  N   LEU   295      41.454  50.334  12.975  1.00  0.00                              
ATOM   3039  CA  LEU   295      42.232  49.481  12.084  1.00  0.00                              
ATOM   3041  CB  LEU   295      42.793  50.331  10.940  1.00  0.00                              
ATOM   3043  C   LEU   295      43.387  48.848  12.850  1.00  0.00                              
ATOM   3045  O   LEU   295      43.896  49.435  13.807  1.00  0.00                              
ATOM   3047  CG  LEU   295      43.458  51.641  11.371  1.00  0.00                              
ATOM   3049  CD1 LEU   295      44.949  51.438  11.601  1.00  0.00                              
ATOM   3051  CD2 LEU   295      43.213  52.732  10.337  1.00  0.00                              
ATOM   3053  H   LYS   296      43.324  47.217  11.742  1.00  0.00                              
ATOM   3055  N   LYS   296      43.783  47.644  12.456  1.00  0.00                              
ATOM   3057  CA  LYS   296      44.917  46.974  13.082  1.00  0.00                              
ATOM   3059  CB  LYS   296      45.375  47.763  14.312  1.00  0.00                              
ATOM   3061  C   LYS   296      44.588  45.536  13.476  1.00  0.00                              
ATOM   3063  O   LYS   296      43.663  45.296  14.255  1.00  0.00                              
ATOM   3065  CG  LYS   296      46.582  47.164  15.017  1.00  0.00                              
ATOM   3067  CD  LYS   296      47.787  47.094  14.088  1.00  0.00                              
ATOM   3069  CE  LYS   296      49.001  46.502  14.791  1.00  0.00                              
ATOM   3071  NZ  LYS   296      50.217  46.542  13.926  1.00  0.00                              
ATOM   3073  H   ASP   297      45.985  44.817  12.289  1.00  0.00                              
ATOM   3075  N   ASP   297      45.338  44.582  12.931  1.00  0.00                              
ATOM   3077  CA  ASP   297      45.173  43.173  13.279  1.00  0.00                              
ATOM   3079  CB  ASP   297      44.347  43.008  14.557  1.00  0.00                              
ATOM   3081  C   ASP   297      44.542  42.380  12.138  1.00  0.00                              
ATOM   3083  O   ASP   297      43.412  42.659  11.734  1.00  0.00                              
ATOM   3085  CG  ASP   297      44.465  41.613  15.142  1.00  0.00                              
ATOM   3087  OD1 ASP   297      45.432  40.900  14.797  1.00  0.00                              
ATOM   3089  OD2 ASP   297      43.582  41.212  15.931  1.00  0.00                              
ATOM   3091  H   HIS   298      46.108  41.187  12.012  1.00  0.00                              
ATOM   3093  N   HIS   298      45.261  41.381  11.638  1.00  0.00                              
ATOM   3095  CA  HIS   298      44.787  40.598  10.501  1.00  0.00                              
ATOM   3097  CB  HIS   298      43.840  41.450   9.648  1.00  0.00                              
ATOM   3099  C   HIS   298      45.978  40.152   9.656  1.00  0.00                              
ATOM   3101  O   HIS   298      46.931  40.913   9.480  1.00  0.00                              
ATOM   3103  CG  HIS   298      42.733  40.678   8.996  1.00  0.00                              
ATOM   3105  ND1 HIS   298      42.209  41.022   7.769  1.00  0.00                              
ATOM   3107  HD1 HIS   298      42.504  41.738   7.218  1.00  0.00                              
ATOM   3109  CE1 HIS   298      41.286  40.139   7.431  1.00  0.00                              
ATOM   3111  NE2 HIS   298      41.100  39.321   8.451  1.00  0.00                              
ATOM   3113  HE2 HIS   298      40.421  38.656   8.497  1.00  0.00                              
ATOM   3115  CD2 HIS   298      41.971  39.658   9.458  1.00  0.00                              
TER 
END
