
#######################################################
#                                                     #
#                        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   23 (   92),  selected   23 , name T0316TS383_3-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS383_3-D3.T0316_D3.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     284      M     284           -
LGA    S     285      S     285           -
LGA    T     286      T     286           -
LGA    S     287      S     287           -
LGA    L     288      L     288           -
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      Q     292           -
LGA    -       -      V     293           -
LGA    -       -      H     294           -
LGA    -       -      F     295           -
LGA    -       -      T     296           -
LGA    -       -      R     297           -
LGA    -       -      E     298           -
LGA    -       -      M     299           -
LGA    -       -      P     300           -
LGA    E     289      E     301          4.564
LGA    A     290      E     302          2.301
LGA    S     291      F     303          3.894
LGA    Q     292      T     304          3.444
LGA    V     293      L     305          2.278
LGA    H     294      E     306          3.369
LGA    F     295      C     307          3.865
LGA    T     296      T     308          2.534
LGA    R     297      A     309          3.183
LGA    E     298      K     310          3.117
LGA    -       -      F     311           -
LGA    M     299      R     312          1.832
LGA    P     300      Y     313          2.422
LGA    E     301      R     314          3.411
LGA    -       -      Q     315           -
LGA    E     302      P     316           #
LGA    -       -      D     317           -
LGA    -       -      S     318           -
LGA    -       -      K     319           -
LGA    -       -      V     320           -
LGA    -       -      T     321           -
LGA    -       -      V     322           -
LGA    -       -      H     323           -
LGA    -       -      V     324           -
LGA    -       -      K     325           -
LGA    -       -      G     326           -
LGA    -       -      E     327           -
LGA    -       -      K     328           -
LGA    -       -      T     329           -
LGA    -       -      E     330           -
LGA    -       -      V     331           -
LGA    -       -      I     332           -
LGA    -       -      F     333           -
LGA    -       -      A     334           -
LGA    -       -      E     335           -
LGA    -       -      P     336           -
LGA    -       -      Q     337           -
LGA    -       -      R     338           -
LGA    -       -      A     339           -
LGA    -       -      I     340           -
LGA    -       -      T     341           -
LGA    -       -      P     342           -
LGA    -       -      G     343           -
LGA    F     303      Q     344          4.753
LGA    T     304      A     345          2.435
LGA    -       -      V     346           -
LGA    -       -      V     347           -
LGA    -       -      F     348           -
LGA    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    -       -      C     354           -
LGA    -       -      L     355           -
LGA    -       -      G     356           -
LGA    L     305      G     357          3.686
LGA    E     306      G     358          4.494
LGA    -       -      L     359           -
LGA    -       -      I     360           -
LGA    -       -      D     361           -
LGA    -       -      N     362           -
LGA    -       -      A     363           -
LGA    -       -      Y     364           -
LGA    -       -      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    -       -      V     369           -
LGA    -       -      C     370           -
LGA    -       -      Q     371           -
LGA    -       -      Y     372           -
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23   90    5.0     17    3.38    11.76     11.222     0.489

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.825620 * X  +   0.201184 * Y  +   0.527140 * Z  + -124.325851
  Y_new =  -0.528942 * X  +   0.601181 * Y  +   0.599001 * Z  +   0.953902
  Z_new =  -0.196397 * X  +  -0.773373 * Y  +   0.602762 * Z  +  28.240425 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.908747    2.232845  [ DEG:   -52.0674    127.9326 ]
  Theta =   0.197682    2.943911  [ DEG:    11.3263    168.6737 ]
  Phi   =  -0.569782    2.571811  [ DEG:   -32.6461    147.3539 ]
 
# 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: T0316TS383_3-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS383_3-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23   90   5.0   17   3.38   11.76  11.222
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS383_3-D3
PFRMAT TS
TARGET T0316
MODEL 3
PARENT 1gpmA
ATOM    897  N   MET   284      15.601  -1.206  -1.711  1.00  0.00
ATOM    898  CA  MET   284      15.303  -2.190  -0.690  1.00  0.00
ATOM    899  C   MET   284      16.206  -3.404  -0.830  1.00  0.00
ATOM    900  O   MET   284      16.530  -4.064   0.162  1.00  0.00
ATOM    901  N   SER   285      16.604  -3.704  -2.063  1.00  0.00
ATOM    902  CA  SER   285      17.480  -4.837  -2.360  1.00  0.00
ATOM    903  C   SER   285      18.873  -4.596  -1.790  1.00  0.00
ATOM    904  O   SER   285      19.482  -5.507  -1.228  1.00  0.00
ATOM    905  N   THR   286      24.442  -9.011   4.944  1.00  0.00
ATOM    906  CA  THR   286      25.786  -9.460   4.593  1.00  0.00
ATOM    907  C   THR   286      26.957  -8.857   5.345  1.00  0.00
ATOM    908  O   THR   286      27.982  -9.528   5.545  1.00  0.00
ATOM    909  N   SER   287      26.838  -7.594   5.739  1.00  0.00
ATOM    910  CA  SER   287      27.927  -6.935   6.449  1.00  0.00
ATOM    911  C   SER   287      27.687  -6.972   7.947  1.00  0.00
ATOM    912  O   SER   287      26.889  -6.204   8.474  1.00  0.00
ATOM    913  N   LEU   288      28.387  -7.871   8.629  1.00  0.00
ATOM    914  CA  LEU   288      28.258  -8.010  10.078  1.00  0.00
ATOM    915  C   LEU   288      28.785  -6.743  10.733  1.00  0.00
ATOM    916  O   LEU   288      29.966  -6.430  10.605  1.00  0.00
ATOM    917  N   GLU   289      27.908  -6.008  11.404  1.00  0.00
ATOM    918  CA  GLU   289      28.320  -4.774  12.051  1.00  0.00
ATOM    919  C   GLU   289      27.454  -3.596  11.637  1.00  0.00
ATOM    920  O   GLU   289      27.568  -2.501  12.198  1.00  0.00
ATOM    921  N   ALA   290      26.619  -3.806  10.619  1.00  0.00
ATOM    922  CA  ALA   290      25.716  -2.769  10.116  1.00  0.00
ATOM    923  C   ALA   290      24.277  -3.282  10.231  1.00  0.00
ATOM    924  O   ALA   290      23.943  -4.344   9.694  1.00  0.00
ATOM    925  N   SER   291      23.440  -2.543  10.954  1.00  0.00
ATOM    926  CA  SER   291      22.050  -2.939  11.155  1.00  0.00
ATOM    927  C   SER   291      21.018  -2.022  10.494  1.00  0.00
ATOM    928  O   SER   291      19.821  -2.338  10.479  1.00  0.00
ATOM    929  N   GLN   292      21.467  -0.898   9.938  1.00  0.00
ATOM    930  CA  GLN   292      20.548   0.030   9.292  1.00  0.00
ATOM    931  C   GLN   292      21.183   0.768   8.128  1.00  0.00
ATOM    932  O   GLN   292      22.362   1.124   8.172  1.00  0.00
ATOM    933  N   VAL   293      20.391   0.994   7.086  1.00  0.00
ATOM    934  CA  VAL   293      20.855   1.704   5.909  1.00  0.00
ATOM    935  C   VAL   293      19.864   2.822   5.641  1.00  0.00
ATOM    936  O   VAL   293      18.651   2.610   5.746  1.00  0.00
ATOM    937  N   HIS   294      20.387   4.013   5.350  1.00  0.00
ATOM    938  CA  HIS   294      19.558   5.187   5.056  1.00  0.00
ATOM    939  C   HIS   294      19.961   5.759   3.697  1.00  0.00
ATOM    940  O   HIS   294      21.023   5.430   3.168  1.00  0.00
ATOM    941  N   PHE   295      19.123   6.623   3.142  1.00  0.00
ATOM    942  CA  PHE   295      19.417   7.209   1.848  1.00  0.00
ATOM    943  C   PHE   295      19.425   8.731   1.923  1.00  0.00
ATOM    944  O   PHE   295      18.519   9.323   2.503  1.00  0.00
ATOM    945  N   THR   296      18.685  12.257   0.879  1.00  0.00
ATOM    946  CA  THR   296      17.700  12.903   0.032  1.00  0.00
ATOM    947  C   THR   296      17.880  14.407   0.068  1.00  0.00
ATOM    948  O   THR   296      16.924  15.166  -0.085  1.00  0.00
ATOM    949  N   ARG   297      19.120  14.830   0.272  1.00  0.00
ATOM    950  CA  ARG   297      19.456  16.245   0.314  1.00  0.00
ATOM    951  C   ARG   297      20.160  16.581  -0.994  1.00  0.00
ATOM    952  O   ARG   297      21.112  15.903  -1.386  1.00  0.00
ATOM    953  N   GLU   298      19.676  17.602  -1.685  1.00  0.00
ATOM    954  CA  GLU   298      20.274  17.993  -2.944  1.00  0.00
ATOM    955  C   GLU   298      21.329  19.066  -2.787  1.00  0.00
ATOM    956  O   GLU   298      21.660  19.485  -1.674  1.00  0.00
ATOM    957  N   MET   299      21.886  19.489  -3.911  1.00  0.00
ATOM    958  CA  MET   299      22.886  20.540  -3.922  1.00  0.00
ATOM    959  C   MET   299      22.406  21.644  -4.855  1.00  0.00
ATOM    960  O   MET   299      22.239  21.422  -6.061  1.00  0.00
ATOM    961  N   PRO   300      22.034  22.797  -4.288  1.00  0.00
ATOM    962  CA  PRO   300      22.049  23.066  -2.848  1.00  0.00
ATOM    963  C   PRO   300      20.751  22.518  -2.231  1.00  0.00
ATOM    964  O   PRO   300      19.934  21.912  -2.931  1.00  0.00
ATOM    965  N   GLU   301      20.540  22.720  -0.920  1.00  0.00
ATOM    966  CA  GLU   301      21.384  23.410   0.056  1.00  0.00
ATOM    967  C   GLU   301      22.484  22.566   0.689  1.00  0.00
ATOM    968  O   GLU   301      23.247  23.064   1.521  1.00  0.00
ATOM    969  N   GLU   302      22.568  21.293   0.321  1.00  0.00
ATOM    970  CA  GLU   302      23.609  20.438   0.879  1.00  0.00
ATOM    971  C   GLU   302      24.691  20.220  -0.174  1.00  0.00
ATOM    972  O   GLU   302      24.516  20.592  -1.331  1.00  0.00
ATOM    973  N   PHE   303      25.829  19.681   0.248  1.00  0.00
ATOM    974  CA  PHE   303      26.927  19.382  -0.661  1.00  0.00
ATOM    975  C   PHE   303      26.824  17.904  -1.022  1.00  0.00
ATOM    976  O   PHE   303      26.040  17.156  -0.405  1.00  0.00
ATOM    977  N   THR   304      29.408  15.597  -0.941  1.00  0.00
ATOM    978  CA  THR   304      30.104  14.864   0.101  1.00  0.00
ATOM    979  C   THR   304      29.610  15.426   1.430  1.00  0.00
ATOM    980  O   THR   304      29.042  16.511   1.470  1.00  0.00
ATOM    981  N   LEU   305      29.739  14.641   2.495  1.00  0.00
ATOM    982  CA  LEU   305      29.300  15.046   3.822  1.00  0.00
ATOM    983  C   LEU   305      30.360  15.796   4.615  1.00  0.00
ATOM    984  O   LEU   305      30.031  16.445   5.616  1.00  0.00
ATOM    985  N   GLU   306      31.617  15.684   4.189  1.00  0.00
ATOM    986  CA  GLU   306      32.739  16.342   4.857  1.00  0.00
ATOM    987  C   GLU   306      33.656  17.011   3.831  1.00  0.00
ATOM    988  O   GLU   306      33.717  16.532   2.676  1.00  0.00
TER
END
