
#######################################################
#                                                     #
#                        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    7 (   35),  selected    7 , name T0347TS261_1_2-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347TS261_1_2-D1.T0347_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    -       -      P       7           -
LGA    -       -      R       8           -
LGA    -       -      L       9           -
LGA    -       -      S      10           -
LGA    -       -      R      11           -
LGA    -       -      I      12           -
LGA    -       -      A      13           -
LGA    -       -      I      14           -
LGA    -       -      D      15           -
LGA    -       -      K      16           -
LGA    -       -      L      17           -
LGA    -       -      R      18           -
LGA    -       -      P      19           -
LGA    -       -      T      20           -
LGA    -       -      Q      21           -
LGA    -       -      I      22           -
LGA    -       -      A      23           -
LGA    -       -      V      24           -
LGA    -       -      G      25           -
LGA    -       -      F      26           -
LGA    -       -      R      27           -
LGA    -       -      E      28           -
LGA    -       -      V      29           -
LGA    -       -      E      30           -
LGA    -       -      L      31           -
LGA    -       -      K      32           -
LGA    -       -      R      33           -
LGA    -       -      K      34           -
LGA    -       -      E      35           -
LGA    -       -      W      36           -
LGA    -       -      R      37           -
LGA    -       -      H      51           -
LGA    -       -      I      52           -
LGA    -       -      V      53           -
LGA    -       -      P      54           -
LGA    -       -      V      55           -
LGA    -       -      V      56           -
LGA    -       -      A      57           -
LGA    -       -      G      58           -
LGA    -       -      P      59           -
LGA    -       -      K      60           -
LGA    -       -      D      61           -
LGA    -       -      R      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      L      65           -
LGA    -       -      I      66           -
LGA    -       -      D      67           -
LGA    -       -      H      68           -
LGA    -       -      H      69           -
LGA    -       -      H      70           -
LGA    -       -      L      71           -
LGA    -       -      V      72           -
LGA    -       -      L      73           -
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    -       -      S      76           -
LGA    -       -      K      77           -
LGA    -       -      E      78           -
LGA    -       -      G      79           -
LGA    -       -      V      80           -
LGA    -       -      E      81           -
LGA    -       -      H      82           -
LGA    -       -      V      83           -
LGA    -       -      L      84           -
LGA    -       -      T      85           -
LGA    -       -      S      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      A      89           -
LGA    -       -      K      90           -
LGA    -       -      F      91           -
LGA    -       -      S      92           -
LGA    -       -      H      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    E      30      K      96          0.578
LGA    L      31      D      97          2.957
LGA    -       -      E      98           -
LGA    -       -      F      99           -
LGA    K      32      W     100          1.267
LGA    R      33      S     101          0.873
LGA    K      34      V     102          0.895
LGA    E      35      M     103          1.406
LGA    W      36      D     104          0.843
LGA    -       -      H     105           -
LGA    -       -      R     106           -
LGA    -       -      N     107           -
LGA    -       -      L     108           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    7   89    5.0      7    1.46     0.00      7.525     0.449

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.092002 * X  +  -0.868196 * Y  +  -0.487618 * Z  +  -7.647672
  Y_new =   0.690102 * X  +  -0.408613 * Y  +   0.597323 * Z  +   1.700968
  Z_new =  -0.717841 * X  +  -0.281551 * Y  +   0.636737 * Z  +  22.463318 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.416330    2.725262  [ DEG:   -23.8540    156.1460 ]
  Theta =   0.800696    2.340897  [ DEG:    45.8765    134.1235 ]
  Phi   =   1.703331   -1.438262  [ DEG:    97.5937    -82.4063 ]
 
# 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: T0347TS261_1_2-D1                             
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS261_1_2-D1.T0347_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    7   89   5.0    7   1.46    0.00   7.525
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS261_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0347
PARENT 1vz0_A
ATOM    387  N   GLU    30      -4.755  30.475   6.468  1.00  5.59
ATOM    388  CA  GLU    30      -4.115  31.767   6.678  1.00  5.59
ATOM    389  C   GLU    30      -3.375  31.715   8.009  1.00  5.59
ATOM    390  O   GLU    30      -3.996  31.637   9.067  1.00  5.59
ATOM    391  CB  GLU    30      -5.157  32.888   6.731  1.00  5.59
ATOM    392  N   LEU    31      -2.050  31.747   7.947  1.00  4.81
ATOM    393  CA  LEU    31      -1.228  31.721   9.148  1.00  4.81
ATOM    394  C   LEU    31      -0.241  32.874   9.056  1.00  4.81
ATOM    395  O   LEU    31       0.970  32.656   9.021  1.00  4.81
ATOM    396  CB  LEU    31      -0.466  30.395   9.236  1.00  4.81
ATOM    397  N   LYS    32      -0.749  34.121   9.022  1.00  6.95
ATOM    398  CA  LYS    32       0.101  35.311   8.923  1.00  6.95
ATOM    399  C   LYS    32       1.293  35.364   9.883  1.00  6.95
ATOM    400  O   LYS    32       2.386  35.797   9.503  1.00  6.95
ATOM    401  CB  LYS    32      -0.896  36.463   9.116  1.00  6.95
ATOM    402  N   ARG    33       1.098  34.919  11.119  1.00  3.25
ATOM    403  CA  ARG    33       2.186  34.930  12.087  1.00  3.25
ATOM    404  C   ARG    33       3.367  34.081  11.589  1.00  3.25
ATOM    405  O   ARG    33       4.513  34.537  11.580  1.00  3.25
ATOM    406  CB  ARG    33       1.694  34.404  13.434  1.00  3.25
ATOM    407  N   LYS    34       3.087  32.849  11.173  1.00  5.67
ATOM    408  CA  LYS    34       4.131  31.959  10.665  1.00  5.67
ATOM    409  C   LYS    34       4.751  32.523   9.389  1.00  5.67
ATOM    410  O   LYS    34       5.956  32.403   9.158  1.00  5.67
ATOM    411  CB  LYS    34       3.557  30.574  10.369  1.00  5.67
ATOM    412  N   GLU    35       3.924  33.138   8.558  1.00  8.01
ATOM    413  CA  GLU    35       4.406  33.722   7.318  1.00  8.01
ATOM    414  C   GLU    35       5.375  34.858   7.623  1.00  8.01
ATOM    415  O   GLU    35       6.425  34.967   6.999  1.00  8.01
ATOM    416  CB  GLU    35       3.223  34.223   6.486  1.00  8.01
ATOM    417  N   TRP    36       5.025  35.702   8.586  1.00  5.34
ATOM    418  CA  TRP    36       5.897  36.810   8.976  1.00  5.34
ATOM    419  C   TRP    36       7.227  36.296   9.547  1.00  5.34
ATOM    420  O   TRP    36       8.288  36.830   9.237  1.00  5.34
ATOM    421  CB  TRP    36       5.196  37.696  10.008  1.00  5.34
TER
END
