
#######################################################
#                                                     #
#                        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   56 (  224),  selected   56 , name T0348TS307_4u
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS307_4u.T0348.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      D       2           -
LGA    -       -      A       3           -
LGA    -       -      K       4           -
LGA    -       -      F       5           -
LGA    -       -      L       6           -
LGA    -       -      E       7           -
LGA    -       -      I       8           -
LGA    L       9      L       9          1.851
LGA    V      10      V      10          1.180
LGA    C      11      C      11          0.759
LGA    P      12      P      12          0.536
LGA    L      13      L      13          0.888
LGA    C      14      C      14          1.406
LGA    K      15      K      15          1.239
LGA    G      16      G      16          1.022
LGA    P      17      P      17          0.807
LGA    L      18      L      18          0.557
LGA    V      19      V      19          1.045
LGA    F      20      F      20          0.685
LGA    D      21      D      21          0.821
LGA    K      22      K      22          0.829
LGA    -       -      S      23           -
LGA    -       -      K      24           -
LGA    D      25      D      25          0.982
LGA    E      26      E      26          0.708
LGA    L      27      L      27          0.563
LGA    I      28      I      28          0.642
LGA    C      29      C      29          1.450
LGA    K      30      K      30          1.935
LGA    G      31      G      31          1.761
LGA    -       -      D      32           -
LGA    R      33      R      33          1.242
LGA    L      34      L      34          1.702
LGA    A      35      A      35          0.834
LGA    F      36      F      36          0.453
LGA    P      37      P      37          1.195
LGA    I      38      I      38          4.161
LGA    K      39      K      39          4.083
LGA    D      40      D      40          1.261
LGA    G      41      G      41          0.880
LGA    I      42      I      42          0.492
LGA    P      43      P      43          0.972
LGA    M      44      M      44          0.939
LGA    M      45      M      45          0.871
LGA    L      46      L      46          1.822
LGA    E      47      E      47          2.907
LGA    S      48      S      48          1.589
LGA    E      49      E      49           -
LGA    A      50      A      50           -
LGA    R      51      R      51           -
LGA    E      52      E      52           -
LGA    L      53      L      53           -
LGA    A      54      A      54           -
LGA    P      55      P      55           -
LGA    E      56      E      56           -
LGA    E      57      E      57           -
LGA    E      58      E      58           -
LGA    V      59      V      59           -
LGA    K      60      K      60           -
LGA    L      61      L      61           -
LGA    E      62      E      62           -
LGA    H      63      -       -           -
LGA    H      64      -       -           -
LGA    H      65      -       -           -
LGA    H      66      -       -           -
LGA    H      67      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   56   61    5.0     37    1.53   100.00     57.104     2.274

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.800050 * X  +   0.562394 * Y  +   0.208884 * Z  + -17.006617
  Y_new =   0.598410 * X  +   0.772875 * Y  +   0.211116 * Z  +   8.040866
  Z_new =  -0.042711 * X  +   0.293902 * Y  +  -0.954881 * Z  +  81.503098 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.843005   -0.298587  [ DEG:   162.8922    -17.1078 ]
  Theta =   0.042724    3.098869  [ DEG:     2.4479    177.5521 ]
  Phi   =   2.499395   -0.642198  [ DEG:   143.2048    -36.7952 ]
 
# 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: T0348TS307_4u                                 
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348TS307_4u.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   56   61   5.0   37   1.53  100.00  57.104
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS307_4u
PFRMAT   TS
TARGET   T0348
MODEL    4  UNREFINED
PARENT   1p91_A
ATOM     1   N   LEU     9      11.993  35.095  57.643  1.00                    
ATOM     1   CA  LEU     9      10.649  34.726  58.069  1.00                    
ATOM     1   C   LEU     9      10.628  33.920  59.363  1.00                    
ATOM     1   O   LEU     9      11.662  33.505  59.875  1.00                    
ATOM     1   N   VAL    10       9.433  33.723  59.898  1.00                    
ATOM     1   CA  VAL    10       9.283  32.933  61.098  1.00                    
ATOM     1   C   VAL    10       8.428  31.756  60.676  1.00                    
ATOM     1   O   VAL    10       7.788  31.805  59.626  1.00                    
ATOM     1   N   CYS    11       8.412  30.688  61.461  1.00                    
ATOM     1   CA  CYS    11       7.612  29.547  61.049  1.00                    
ATOM     1   C   CYS    11       6.152  29.805  61.337  1.00                    
ATOM     1   O   CYS    11       5.790  30.176  62.444  1.00                    
ATOM     1   N   PRO    12       5.291  29.643  60.328  1.00                    
ATOM     1   CA  PRO    12       3.869  29.871  60.562  1.00                    
ATOM     1   C   PRO    12       3.425  28.988  61.704  1.00                    
ATOM     1   O   PRO    12       2.457  29.309  62.397  1.00                    
ATOM     1   N   LEU    13       4.155  27.887  61.908  1.00                    
ATOM     1   CA  LEU    13       3.829  26.929  62.959  1.00                    
ATOM     1   C   LEU    13       4.621  26.953  64.271  1.00                    
ATOM     1   O   LEU    13       4.005  27.008  65.341  1.00                    
ATOM     1   N   CYS    14       5.954  26.885  64.226  1.00                    
ATOM     1   CA  CYS    14       6.710  26.911  65.482  1.00                    
ATOM     1   C   CYS    14       7.261  28.290  65.771  1.00                    
ATOM     1   O   CYS    14       7.869  28.524  66.821  1.00                    
ATOM     1   N   LYS    15       7.049  29.197  64.828  1.00                    
ATOM     1   CA  LYS    15       7.504  30.564  64.987  1.00                    
ATOM     1   C   LYS    15       9.011  30.690  65.198  1.00                    
ATOM     1   O   LYS    15       9.464  31.546  65.970  1.00                    
ATOM     1   N   GLY    16       9.785  29.832  64.538  1.00                    
ATOM     1   CA  GLY    16      11.235  29.894  64.648  1.00                    
ATOM     1   C   GLY    16      11.782  30.289  63.297  1.00                    
ATOM     1   O   GLY    16      11.133  30.103  62.278  1.00                    
ATOM     1   N   PRO    17      12.985  30.846  63.267  1.00                    
ATOM     1   CA  PRO    17      13.603  31.281  62.022  1.00                    
ATOM     1   C   PRO    17      13.470  30.335  60.852  1.00                    
ATOM     1   O   PRO    17      13.748  29.153  60.968  1.00                    
ATOM     1   N   LEU    18      13.044  30.856  59.715  1.00                    
ATOM     1   CA  LEU    18      12.929  30.019  58.543  1.00                    
ATOM     1   C   LEU    18      14.218  30.113  57.737  1.00                    
ATOM     1   O   LEU    18      14.491  31.124  57.094  1.00                    
ATOM     1   N   VAL    19      15.012  29.052  57.798  1.00                    
ATOM     1   CA  VAL    19      16.264  28.964  57.063  1.00                    
ATOM     1   C   VAL    19      15.887  28.524  55.660  1.00                    
ATOM     1   O   VAL    19      14.978  27.712  55.491  1.00                    
ATOM     1   N   PHE    20      16.566  29.055  54.654  1.00                    
ATOM     1   CA  PHE    20      16.238  28.694  53.279  1.00                    
ATOM     1   C   PHE    20      17.218  27.793  52.549  1.00                    
ATOM     1   O   PHE    20      18.415  28.029  52.613  1.00                    
ATOM     1   N   ASP    21      16.704  26.785  51.835  1.00                    
ATOM     1   CA  ASP    21      17.531  25.859  51.043  1.00                    
ATOM     1   C   ASP    21      17.005  25.879  49.614  1.00                    
ATOM     1   O   ASP    21      15.904  25.426  49.324  1.00                    
ATOM     1   N   LYS    22      17.820  26.424  48.727  1.00                    
ATOM     1   CA  LYS    22      17.471  26.615  47.328  1.00                    
ATOM     1   C   LYS    22      16.146  27.360  47.204  1.00                    
ATOM     1   O   LYS    22      16.127  28.594  47.194  1.00                    
ATOM     1   N   ASP    25      15.039  26.630  47.100  1.00                    
ATOM     1   CA  ASP    25      13.742  27.287  46.979  1.00                    
ATOM     1   C   ASP    25      12.719  26.797  47.969  1.00                    
ATOM     1   O   ASP    25      11.533  26.726  47.679  1.00                    
ATOM     1   N   GLU    26      13.195  26.462  49.153  1.00                    
ATOM     1   CA  GLU    26      12.314  26.009  50.209  1.00                    
ATOM     1   C   GLU    26      12.746  26.683  51.504  1.00                    
ATOM     1   O   GLU    26      13.909  27.061  51.673  1.00                    
ATOM     1   N   LEU    27      11.801  26.862  52.411  1.00                    
ATOM     1   CA  LEU    27      12.115  27.449  53.699  1.00                    
ATOM     1   C   LEU    27      11.908  26.330  54.697  1.00                    
ATOM     1   O   LEU    27      10.900  25.618  54.643  1.00                    
ATOM     1   N   ILE    28      12.881  26.143  55.575  1.00                    
ATOM     1   CA  ILE    28      12.793  25.085  56.560  1.00                    
ATOM     1   C   ILE    28      13.079  25.647  57.905  1.00                    
ATOM     1   O   ILE    28      13.979  26.439  58.032  1.00                    
ATOM     1   N   CYS    29      12.339  25.246  58.920  1.00                    
ATOM     1   CA  CYS    29      12.660  25.735  60.249  1.00                    
ATOM     1   C   CYS    29      13.309  24.622  61.101  1.00                    
ATOM     1   O   CYS    29      13.328  23.443  60.727  1.00                    
ATOM     1   N   LYS    30      13.886  24.998  62.246  1.00                    
ATOM     1   CA  LYS    30      14.523  24.031  63.125  1.00                    
ATOM     1   C   LYS    30      13.758  22.743  63.339  1.00                    
ATOM     1   O   LYS    30      14.366  21.677  63.457  1.00                    
ATOM     1   N   GLY    31      12.432  22.822  63.378  1.00                    
ATOM     1   CA  GLY    31      11.652  21.620  63.608  1.00                    
ATOM     1   C   GLY    31      11.060  20.991  62.367  1.00                    
ATOM     1   O   GLY    31       9.957  20.455  62.385  1.00                    
ATOM     1   N   ARG    33      11.835  21.067  61.292  1.00                    
ATOM     1   CA  ARG    33      11.503  20.457  60.013  1.00                    
ATOM     1   C   ARG    33      10.145  20.786  59.453  1.00                    
ATOM     1   O   ARG    33       9.345  19.897  59.205  1.00                    
ATOM     1   N   LEU    34       9.888  22.079  59.287  1.00                    
ATOM     1   CA  LEU    34       8.656  22.583  58.691  1.00                    
ATOM     1   C   LEU    34       9.192  23.186  57.400  1.00                    
ATOM     1   O   LEU    34      10.064  24.053  57.417  1.00                    
ATOM     1   N   ALA    35       8.704  22.690  56.278  1.00                    
ATOM     1   CA  ALA    35       9.195  23.159  54.998  1.00                    
ATOM     1   C   ALA    35       8.112  23.861  54.203  1.00                    
ATOM     1   O   ALA    35       6.976  23.396  54.141  1.00                    
ATOM     1   N   PHE    36       8.454  25.004  53.624  1.00                    
ATOM     1   CA  PHE    36       7.501  25.733  52.812  1.00                    
ATOM     1   C   PHE    36       8.176  26.004  51.483  1.00                    
ATOM     1   O   PHE    36       9.224  26.636  51.424  1.00                    
ATOM     1   N   PRO    37       7.581  25.497  50.416  1.00                    
ATOM     1   CA  PRO    37       8.141  25.673  49.092  1.00                    
ATOM     1   C   PRO    37       7.638  26.926  48.428  1.00                    
ATOM     1   O   PRO    37       6.590  27.474  48.791  1.00                    
ATOM     1   N   ILE    38       6.177  28.824  45.206  1.00                    
ATOM     1   CA  ILE    38       5.422  28.550  43.990  1.00                    
ATOM     1   C   ILE    38       6.275  28.979  42.798  1.00                    
ATOM     1   O   ILE    38       7.196  29.789  42.941  1.00                    
ATOM     1   N   LYS    39       5.965  28.434  41.625  1.00                    
ATOM     1   CA  LYS    39       6.736  28.722  40.424  1.00                    
ATOM     1   C   LYS    39       6.962  30.195  40.172  1.00                    
ATOM     1   O   LYS    39       8.022  30.578  39.679  1.00                    
ATOM     1   N   ASP    40       5.977  31.015  40.526  1.00                    
ATOM     1   CA  ASP    40       6.062  32.464  40.334  1.00                    
ATOM     1   C   ASP    40       7.051  33.184  41.270  1.00                    
ATOM     1   O   ASP    40       7.656  34.188  40.893  1.00                    
ATOM     1   N   GLY    41       7.198  32.691  42.495  1.00                    
ATOM     1   CA  GLY    41       8.134  33.306  43.415  1.00                    
ATOM     1   C   GLY    41       7.653  33.629  44.816  1.00                    
ATOM     1   O   GLY    41       8.448  34.044  45.653  1.00                    
ATOM     1   N   ILE    42       6.372  33.453  45.105  1.00                    
ATOM     1   CA  ILE    42       5.931  33.781  46.453  1.00                    
ATOM     1   C   ILE    42       6.156  32.653  47.416  1.00                    
ATOM     1   O   ILE    42       6.652  31.612  47.049  1.00                    
ATOM     1   N   PRO    43       5.775  32.863  48.657  1.00                    
ATOM     1   CA  PRO    43       5.966  31.857  49.672  1.00                    
ATOM     1   C   PRO    43       4.654  31.675  50.370  1.00                    
ATOM     1   O   PRO    43       4.257  32.542  51.140  1.00                    
ATOM     1   N   MET    44       3.953  30.579  50.123  1.00                    
ATOM     1   CA  MET    44       2.693  30.441  50.830  1.00                    
ATOM     1   C   MET    44       3.093  30.148  52.250  1.00                    
ATOM     1   O   MET    44       4.086  29.469  52.471  1.00                    
ATOM     1   N   MET    45       2.347  30.659  53.213  1.00                    
ATOM     1   CA  MET    45       2.691  30.432  54.608  1.00                    
ATOM     1   C   MET    45       1.453  30.189  55.450  1.00                    
ATOM     1   O   MET    45       1.496  30.279  56.677  1.00                    
ATOM     1   N   LEU    46       0.349  29.863  54.793  1.00                    
ATOM     1   CA  LEU    46      -0.906  29.635  55.499  1.00                    
ATOM     1   C   LEU    46      -1.028  28.165  55.900  1.00                    
ATOM     1   O   LEU    46      -0.127  27.366  55.610  1.00                    
ATOM     1   N   GLU    47      -2.119  27.799  56.619  1.00                    
ATOM     1   CA  GLU    47      -2.303  26.399  57.008  1.00                    
ATOM     1   C   GLU    47      -2.532  25.615  55.715  1.00                    
ATOM     1   O   GLU    47      -2.248  26.095  54.617  1.00                    
ATOM     1   N   SER    48      -3.080  24.418  55.842  1.00                    
ATOM     1   CA  SER    48      -3.311  23.589  54.668  1.00                    
ATOM     1   C   SER    48      -4.742  23.615  54.097  1.00                    
ATOM     1   O   SER    48      -4.919  23.584  52.875  1.00                    
ATOM     1   N   GLU    49      -5.758  23.703  54.956  1.00                    
ATOM     1   CA  GLU    49      -7.135  23.669  54.458  1.00                    
ATOM     1   C   GLU    49      -8.211  24.333  55.314  1.00                    
ATOM     1   O   GLU    49      -9.232  23.701  55.637  1.00                    
ATOM     1   N   ALA    50      -8.009  25.596  55.686  1.00                    
ATOM     1   CA  ALA    50      -9.042  26.251  56.479  1.00                    
ATOM     1   C   ALA    50      -9.458  27.659  56.032  1.00                    
ATOM     1   O   ALA    50      -8.620  28.567  55.895  1.00                    
ATOM     1   N   ARG    51     -10.768  27.817  55.826  1.00                    
ATOM     1   CA  ARG    51     -11.349  29.080  55.395  1.00                    
ATOM     1   C   ARG    51     -10.785  29.538  54.054  1.00                    
ATOM     1   O   ARG    51     -11.184  30.584  53.534  1.00                    
ATOM     1   N   GLU    52      -9.844  28.767  53.507  1.00                    
ATOM     1   CA  GLU    52      -9.283  29.088  52.196  1.00                    
ATOM     1   C   GLU    52     -10.540  29.103  51.327  1.00                    
ATOM     1   O   GLU    52     -10.729  29.987  50.479  1.00                    
ATOM     1   N   LEU    53     -11.403  28.113  51.596  1.00                    
ATOM     1   CA  LEU    53     -12.721  27.984  50.957  1.00                    
ATOM     1   C   LEU    53     -13.444  29.241  51.456  1.00                    
ATOM     1   O   LEU    53     -13.486  29.520  52.669  1.00                    
ATOM     1   N   ALA    54     -14.019  30.012  50.542  1.00                    
ATOM     1   CA  ALA    54     -14.618  31.237  51.008  1.00                    
ATOM     1   C   ALA    54     -15.906  31.809  50.527  1.00                    
ATOM     1   O   ALA    54     -16.758  31.190  49.855  1.00                    
ATOM     1   N   PRO    55     -16.031  33.071  50.953  1.00                    
ATOM     1   CA  PRO    55     -17.153  33.961  50.613  1.00                    
ATOM     1   C   PRO    55     -16.327  35.211  50.189  1.00                    
ATOM     1   O   PRO    55     -16.409  36.252  50.854  1.00                    
ATOM     1   N   GLU    56     -15.575  35.107  49.020  1.00                    
ATOM     1   CA  GLU    56     -14.696  36.200  48.523  1.00                    
ATOM     1   C   GLU    56     -15.029  37.675  48.610  1.00                    
ATOM     1   O   GLU    56     -14.951  38.326  49.688  1.00                    
ATOM     1   N   GLU    57     -15.373  38.202  47.462  1.00                    
ATOM     1   CA  GLU    57     -15.732  39.586  47.338  1.00                    
ATOM     1   C   GLU    57     -14.499  40.084  46.654  1.00                    
ATOM     1   O   GLU    57     -14.534  41.001  45.836  1.00                    
ATOM     1   N   GLU    58     -13.406  39.406  47.002  1.00                    
ATOM     1   CA  GLU    58     -12.088  39.668  46.476  1.00                    
ATOM     1   C   GLU    58     -11.475  38.469  45.751  1.00                    
ATOM     1   O   GLU    58     -10.390  38.006  46.098  1.00                    
ATOM     1   N   VAL    59     -12.169  37.981  44.730  1.00                    
ATOM     1   CA  VAL    59     -11.645  36.873  43.954  1.00                    
ATOM     1   C   VAL    59     -11.160  37.438  42.624  1.00                    
ATOM     1   O   VAL    59     -11.539  38.542  42.253  1.00                    
ATOM     1   N   LYS    60     -10.330  36.674  41.925  1.00                    
ATOM     1   CA  LYS    60      -9.754  37.089  40.645  1.00                    
ATOM     1   C   LYS    60     -10.458  38.221  39.913  1.00                    
ATOM     1   O   LYS    60      -9.830  39.201  39.533  1.00                    
ATOM     1   N   LEU    61     -11.760  38.086  39.708  1.00                    
ATOM     1   CA  LEU    61     -12.520  39.110  38.999  1.00                    
ATOM     1   C   LEU    61     -12.274  40.517  39.531  1.00                    
ATOM     1   O   LEU    61     -11.833  41.408  38.798  1.00                    
ATOM     1   N   GLU    62      -8.614  41.893  39.648  1.00                    
ATOM     1   CA  GLU    62      -8.264  42.452  38.352  1.00                    
ATOM     1   C   GLU    62      -8.852  43.842  38.229  1.00                    
ATOM     1   O   GLU    62      -8.374  44.647  37.434  1.00                    
ATOM     1   N   HIS    63      -9.905  44.118  39.002  1.00                    
ATOM     1   CA  HIS    63     -10.545  45.439  38.984  1.00                    
ATOM     1   C   HIS    63      -9.694  46.414  39.789  1.00                    
ATOM     1   O   HIS    63      -9.082  47.327  39.210  1.00                    
ATOM     1   N   HIS    64      -9.655  46.231  41.116  1.00                    
ATOM     1   CA  HIS    64      -8.835  47.095  41.964  1.00                    
ATOM     1   C   HIS    64      -7.585  47.366  41.139  1.00                    
ATOM     1   O   HIS    64      -7.167  48.508  40.956  1.00                    
ATOM     1   N   HIS    65      -7.020  46.296  40.603  1.00                    
ATOM     1   CA  HIS    65      -5.833  46.424  39.797  1.00                    
ATOM     1   C   HIS    65      -6.053  47.339  38.612  1.00                    
ATOM     1   O   HIS    65      -5.487  48.421  38.545  1.00                    
ATOM     1   N   HIS    66      -6.876  46.912  37.671  1.00                    
ATOM     1   CA  HIS    66      -7.114  47.723  36.493  1.00                    
ATOM     1   C   HIS    66      -7.432  49.178  36.851  1.00                    
ATOM     1   O   HIS    66      -7.059  50.090  36.105  1.00                    
ATOM     1   N   HIS    67      -8.101  49.396  37.990  1.00                    
ATOM     1   CA  HIS    67      -8.450  50.753  38.433  1.00                    
ATOM     1   C   HIS    67      -7.221  51.532  38.839  1.00                    
ATOM     1   O   HIS    67      -7.033  52.679  38.445  1.00                    
TER
END
