
#######################################################
#                                                     #
#                        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 T0363TS307_3u-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS307_3u-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N      11           -
LGA    Q      12      Q      12          1.258
LGA    I      13      I      13          1.895
LGA    N      14      N      14          0.713
LGA    I      15      I      15          0.712
LGA    E      16      E      16          2.176
LGA    I      17      I      17          2.259
LGA    A      18      A      18          2.594
LGA    Y      19      Y      19          2.540
LGA    A      20      A      20          1.714
LGA    F      21      F      21          3.781
LGA    P      22      P      22          3.276
LGA    E      23      E      23           -
LGA    R      24      R      24          3.706
LGA    Y      25      Y      25          5.033
LGA    Y      26      Y      26           #
LGA    L      27      L      27           #
LGA    K      28      K      28          1.418
LGA    S      29      S      29          0.673
LGA    F      30      F      30          1.315
LGA    Q      31      Q      31          1.404
LGA    V      32      V      32          1.466
LGA    D      33      D      33          1.450
LGA    E      34      E      34          2.156
LGA    G      35      G      35          0.635
LGA    I      36      I      36          0.436
LGA    T      37      T      37          0.261
LGA    V      38      V      38          0.332
LGA    Q      39      Q      39          0.554
LGA    T      40      T      40          0.737
LGA    A      41      A      41          1.187
LGA    I      42      I      42          1.125
LGA    T      43      T      43          0.648
LGA    Q      44      Q      44          2.102
LGA    I      47      S      45          2.738
LGA    L      48      G      46          2.474
LGA    S      49      -       -           -
LGA    Q      50      I      47          5.590
LGA    F      51      L      48           #
LGA    P      52      S      49          2.207
LGA    E      53      Q      50          1.957
LGA    I      54      F      51          2.715
LGA    D      55      P      52          4.156
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    -       -      D      55           -
LGA    L      56      L      56          1.986

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43   46    5.0     38    2.31    81.58     60.887     1.577

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.492240 * X  +  -0.850047 * Y  +  -0.187405 * Z  +  50.597427
  Y_new =   0.805035 * X  +   0.362677 * Y  +   0.469450 * Z  + -25.613321
  Z_new =  -0.331087 * X  +  -0.381950 * Y  +   0.862842 * Z  +  33.575500 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.416737    2.724855  [ DEG:   -23.8773    156.1227 ]
  Theta =   0.337455    2.804137  [ DEG:    19.3348    160.6652 ]
  Phi   =   1.021999   -2.119593  [ DEG:    58.5563   -121.4437 ]
 
# 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: T0363TS307_3u-D1                              
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS307_3u-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43   46   5.0   38   2.31   81.58  60.887
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS307_3u-D1
PFRMAT   TS
TARGET   T0363
MODEL    3  UNREFINED
PARENT   1vjk_A
ATOM     1   N   GLN    12      17.755   1.439   9.112  1.00                    
ATOM     1   CA  GLN    12      18.476   2.556   8.403  1.00                    
ATOM     1   C   GLN    12      17.999   3.951   8.841  1.00                    
ATOM     1   O   GLN    12      16.829   4.146   9.216  1.00                    
ATOM     1   N   ILE    13      18.923   4.911   8.803  1.00                    
ATOM     1   CA  ILE    13      18.642   6.318   9.100  1.00                    
ATOM     1   C   ILE    13      18.995   7.101   7.822  1.00                    
ATOM     1   O   ILE    13      20.147   7.057   7.382  1.00                    
ATOM     1   N   ASN    14      18.021   7.784   7.221  1.00                    
ATOM     1   CA  ASN    14      18.279   8.541   6.005  1.00                    
ATOM     1   C   ASN    14      18.322  10.015   6.327  1.00                    
ATOM     1   O   ASN    14      17.326  10.578   6.836  1.00                    
ATOM     1   N   ILE    15      19.457  10.646   6.059  1.00                    
ATOM     1   CA  ILE    15      19.623  12.069   6.334  1.00                    
ATOM     1   C   ILE    15      19.760  12.828   5.031  1.00                    
ATOM     1   O   ILE    15      20.229  12.281   4.005  1.00                    
ATOM     1   N   GLU    16      19.355  14.081   5.034  1.00                    
ATOM     1   CA  GLU    16      19.478  14.953   3.894  1.00                    
ATOM     1   C   GLU    16      20.675  15.829   4.136  1.00                    
ATOM     1   O   GLU    16      20.679  16.623   5.087  1.00                    
ATOM     1   N   ILE    17      21.690  15.714   3.300  1.00                    
ATOM     1   CA  ILE    17      22.892  16.525   3.408  1.00                    
ATOM     1   C   ILE    17      22.820  17.688   2.451  1.00                    
ATOM     1   O   ILE    17      22.567  17.475   1.264  1.00                    
ATOM     1   N   ALA    18      23.007  18.911   2.963  1.00                    
ATOM     1   CA  ALA    18      23.001  20.114   2.125  1.00                    
ATOM     1   C   ALA    18      24.401  20.686   2.132  1.00                    
ATOM     1   O   ALA    18      24.943  21.028   3.198  1.00                    
ATOM     1   N   TYR    19      24.994  20.788   0.954  1.00                    
ATOM     1   CA  TYR    19      26.325  21.379   0.801  1.00                    
ATOM     1   C   TYR    19      26.213  22.835   0.453  1.00                    
ATOM     1   O   TYR    19      25.294  23.249  -0.276  1.00                    
ATOM     1   N   ALA    20      27.186  23.611   0.945  1.00                    
ATOM     1   CA  ALA    20      27.207  25.042   0.715  1.00                    
ATOM     1   C   ALA    20      28.497  25.509   0.100  1.00                    
ATOM     1   O   ALA    20      29.559  24.941   0.344  1.00                    
ATOM     1   N   PHE    21      28.400  26.589  -0.674  1.00                    
ATOM     1   CA  PHE    21      29.569  27.281  -1.210  1.00                    
ATOM     1   C   PHE    21      30.484  26.294  -1.952  1.00                    
ATOM     1   O   PHE    21      29.988  25.520  -2.781  1.00                    
ATOM     1   N   PRO    22      31.794  26.302  -1.681  1.00                    
ATOM     1   CA  PRO    22      32.679  25.484  -2.535  1.00                    
ATOM     1   C   PRO    22      32.442  24.001  -2.367  1.00                    
ATOM     1   O   PRO    22      32.810  23.214  -3.236  1.00                    
ATOM     1   N   GLU    23      31.797  23.605  -1.272  1.00                    
ATOM     1   CA  GLU    23      31.540  22.174  -1.030  1.00                    
ATOM     1   C   GLU    23      30.490  21.615  -1.961  1.00                    
ATOM     1   O   GLU    23      30.427  20.397  -2.142  1.00                    
ATOM     1   N   ARG    24      29.710  22.490  -2.590  1.00                    
ATOM     1   CA  ARG    24      28.816  22.063  -3.672  1.00                    
ATOM     1   C   ARG    24      29.623  21.545  -4.850  1.00                    
ATOM     1   O   ARG    24      29.184  20.600  -5.522  1.00                    
ATOM     1   N   TYR    25      30.774  22.166  -5.148  1.00                    
ATOM     1   CA  TYR    25      31.622  21.655  -6.205  1.00                    
ATOM     1   C   TYR    25      32.344  20.414  -5.820  1.00                    
ATOM     1   O   TYR    25      32.491  19.532  -6.652  1.00                    
ATOM     1   N   TYR    26      32.810  20.323  -4.571  1.00                    
ATOM     1   CA  TYR    26      33.490  19.098  -4.147  1.00                    
ATOM     1   C   TYR    26      32.555  17.894  -4.147  1.00                    
ATOM     1   O   TYR    26      32.966  16.789  -4.500  1.00                    
ATOM     1   N   LEU    27      31.307  18.091  -3.708  1.00                    
ATOM     1   CA  LEU    27      30.344  16.998  -3.696  1.00                    
ATOM     1   C   LEU    27      29.767  16.716  -5.077  1.00                    
ATOM     1   O   LEU    27      29.257  15.616  -5.329  1.00                    
ATOM     1   N   LYS    28      22.183  15.821  -1.058  1.00                    
ATOM     1   CA  LYS    28      22.108  14.392  -1.284  1.00                    
ATOM     1   C   LYS    28      21.560  13.693  -0.073  1.00                    
ATOM     1   O   LYS    28      21.806  14.122   1.061  1.00                    
ATOM     1   N   SER    29      20.799  12.642  -0.300  1.00                    
ATOM     1   CA  SER    29      20.301  11.796   0.755  1.00                    
ATOM     1   C   SER    29      21.292  10.712   1.043  1.00                    
ATOM     1   O   SER    29      21.734  10.000   0.114  1.00                    
ATOM     1   N   PHE    30      21.626  10.521   2.307  1.00                    
ATOM     1   CA  PHE    30      22.575   9.504   2.692  1.00                    
ATOM     1   C   PHE    30      21.941   8.556   3.696  1.00                    
ATOM     1   O   PHE    30      21.539   8.957   4.807  1.00                    
ATOM     1   N   GLN    31      21.819   7.300   3.301  1.00                    
ATOM     1   CA  GLN    31      21.314   6.244   4.169  1.00                    
ATOM     1   C   GLN    31      22.468   5.702   5.011  1.00                    
ATOM     1   O   GLN    31      23.527   5.353   4.483  1.00                    
ATOM     1   N   VAL    32      22.254   5.657   6.324  1.00                    
ATOM     1   CA  VAL    32      23.262   5.253   7.279  1.00                    
ATOM     1   C   VAL    32      22.715   4.121   8.128  1.00                    
ATOM     1   O   VAL    32      21.509   4.024   8.303  1.00                    
ATOM     1   N   ASP    33      23.579   3.249   8.657  1.00                    
ATOM     1   CA  ASP    33      23.115   2.172   9.528  1.00                    
ATOM     1   C   ASP    33      22.552   2.695  10.840  1.00                    
ATOM     1   O   ASP    33      22.902   3.788  11.301  1.00                    
ATOM     1   N   GLU    34      21.673   1.896  11.429  1.00                    
ATOM     1   CA  GLU    34      21.158   2.135  12.759  1.00                    
ATOM     1   C   GLU    34      22.287   2.550  13.710  1.00                    
ATOM     1   O   GLU    34      23.359   1.952  13.706  1.00                    
ATOM     1   N   GLY    35      22.027   3.590  14.500  1.00                    
ATOM     1   CA  GLY    35      22.975   4.055  15.504  1.00                    
ATOM     1   C   GLY    35      23.990   5.050  14.972  1.00                    
ATOM     1   O   GLY    35      24.887   5.497  15.707  1.00                    
ATOM     1   N   ILE    36      23.870   5.411  13.702  1.00                    
ATOM     1   CA  ILE    36      24.841   6.314  13.111  1.00                    
ATOM     1   C   ILE    36      24.938   7.613  13.852  1.00                    
ATOM     1   O   ILE    36      23.929   8.187  14.296  1.00                    
ATOM     1   N   THR    37      26.177   8.091  13.944  1.00                    
ATOM     1   CA  THR    37      26.502   9.351  14.583  1.00                    
ATOM     1   C   THR    37      27.021  10.354  13.556  1.00                    
ATOM     1   O   THR    37      27.400   9.994  12.430  1.00                    
ATOM     1   N   VAL    38      27.097  11.624  13.936  1.00                    
ATOM     1   CA  VAL    38      27.675  12.646  13.062  1.00                    
ATOM     1   C   VAL    38      29.044  12.218  12.499  1.00                    
ATOM     1   O   VAL    38      29.308  12.359  11.284  1.00                    
ATOM     1   N   GLN    39      29.916  11.656  13.348  1.00                    
ATOM     1   CA  GLN    39      31.228  11.244  12.844  1.00                    
ATOM     1   C   GLN    39      31.125  10.179  11.722  1.00                    
ATOM     1   O   GLN    39      31.962  10.154  10.805  1.00                    
ATOM     1   N   THR    40      30.112   9.308  11.802  1.00                    
ATOM     1   CA  THR    40      29.933   8.267  10.765  1.00                    
ATOM     1   C   THR    40      29.485   8.901   9.483  1.00                    
ATOM     1   O   THR    40      29.923   8.484   8.403  1.00                    
ATOM     1   N   ALA    41      28.639   9.913   9.578  1.00                    
ATOM     1   CA  ALA    41      28.215  10.640   8.381  1.00                    
ATOM     1   C   ALA    41      29.395  11.353   7.711  1.00                    
ATOM     1   O   ALA    41      29.534  11.286   6.476  1.00                    
ATOM     1   N   ILE    42      30.264  11.978   8.505  1.00                    
ATOM     1   CA  ILE    42      31.444  12.628   7.949  1.00                    
ATOM     1   C   ILE    42      32.304  11.607   7.209  1.00                    
ATOM     1   O   ILE    42      32.783  11.875   6.077  1.00                    
ATOM     1   N   THR    43      32.512  10.421   7.806  1.00                    
ATOM     1   CA  THR    43      33.273   9.391   7.088  1.00                    
ATOM     1   C   THR    43      32.628   8.948   5.796  1.00                    
ATOM     1   O   THR    43      33.344   8.671   4.809  1.00                    
ATOM     1   N   GLN    44      31.305   8.878   5.772  1.00                    
ATOM     1   CA  GLN    44      30.612   8.487   4.559  1.00                    
ATOM     1   C   GLN    44      30.714   9.574   3.488  1.00                    
ATOM     1   O   GLN    44      30.861   9.239   2.307  1.00                    
ATOM     1   N   ILE    47      30.659  10.863   3.872  1.00                    
ATOM     1   CA  ILE    47      30.844  11.942   2.893  1.00                    
ATOM     1   C   ILE    47      32.219  11.815   2.234  1.00                    
ATOM     1   O   ILE    47      32.331  11.905   0.992  1.00                    
ATOM     1   N   LEU    48      33.235  11.558   3.052  1.00                    
ATOM     1   CA  LEU    48      34.601  11.378   2.549  1.00                    
ATOM     1   C   LEU    48      34.733  10.151   1.635  1.00                    
ATOM     1   O   LEU    48      35.506  10.183   0.650  1.00                    
ATOM     1   N   SER    49      33.990   9.090   1.941  1.00                    
ATOM     1   CA  SER    49      34.008   7.886   1.128  1.00                    
ATOM     1   C   SER    49      33.345   8.126  -0.225  1.00                    
ATOM     1   O   SER    49      33.809   7.607  -1.251  1.00                    
ATOM     1   N   GLN    50      32.252   8.886  -0.250  1.00                    
ATOM     1   CA  GLN    50      31.546   9.146  -1.492  1.00                    
ATOM     1   C   GLN    50      32.264  10.164  -2.365  1.00                    
ATOM     1   O   GLN    50      32.158  10.144  -3.590  1.00                    
ATOM     1   N   PHE    51      32.927  11.106  -1.711  1.00                    
ATOM     1   CA  PHE    51      33.500  12.260  -2.392  1.00                    
ATOM     1   C   PHE    51      34.907  12.467  -1.895  1.00                    
ATOM     1   O   PHE    51      35.139  13.212  -0.910  1.00                    
ATOM     1   N   PRO    52      35.857  11.836  -2.584  1.00                    
ATOM     1   CA  PRO    52      37.232  11.759  -2.086  1.00                    
ATOM     1   C   PRO    52      37.896  13.112  -1.874  1.00                    
ATOM     1   O   PRO    52      38.823  13.208  -1.075  1.00                    
ATOM     1   N   GLU    53      37.420  14.151  -2.556  1.00                    
ATOM     1   CA  GLU    53      38.018  15.492  -2.366  1.00                    
ATOM     1   C   GLU    53      37.802  16.014  -0.945  1.00                    
ATOM     1   O   GLU    53      38.525  16.916  -0.499  1.00                    
ATOM     1   N   ILE    54      36.841  15.441  -0.203  1.00                    
ATOM     1   CA  ILE    54      36.643  15.834   1.192  1.00                    
ATOM     1   C   ILE    54      37.644  15.205   2.160  1.00                    
ATOM     1   O   ILE    54      37.720  15.612   3.327  1.00                    
ATOM     1   N   ASP    55      38.395  14.203   1.711  1.00                    
ATOM     1   CA  ASP    55      39.338  13.535   2.618  1.00                    
ATOM     1   C   ASP    55      40.373  14.521   3.158  1.00                    
ATOM     1   O   ASP    55      40.799  14.395   4.315  1.00                    
ATOM     1   N   LEU    56      37.289  18.737   9.035  1.00                    
ATOM     1   CA  LEU    56      35.982  18.994   9.649  1.00                    
ATOM     1   C   LEU    56      36.157  19.389  11.098  1.00                    
ATOM     1   O   LEU    56      36.915  18.766  11.844  1.00                    
TER
END
