
#######################################################
#                                                     #
#                        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   16 (   64),  selected   16 , name T0316TS307_5u-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS307_5u-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           -
LGA    -       -      S     285           -
LGA    -       -      T     286           -
LGA    -       -      S     287           -
LGA    -       -      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     301           -
LGA    -       -      E     302           -
LGA    -       -      F     303           -
LGA    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      T     308           -
LGA    -       -      A     309           -
LGA    -       -      K     310           -
LGA    -       -      F     311           -
LGA    -       -      R     312           -
LGA    M     284      Y     313          0.943
LGA    S     285      R     314          3.910
LGA    T     286      Q     315           -
LGA    S     287      P     316           -
LGA    L     288      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    E     289      P     342          4.883
LGA    -       -      G     343           -
LGA    H     294      Q     344          2.826
LGA    -       -      A     345           -
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    -       -      G     357           -
LGA    -       -      G     358           -
LGA    -       -      L     359           -
LGA    F     295      I     360          0.831
LGA    T     296      D     361          2.310
LGA    R     297      N     362          2.779
LGA    E     298      A     363          1.527
LGA    M     299      Y     364          1.352
LGA    P     300      R     365          1.132
LGA    E     301      D     366          2.837
LGA    E     302      G     367          2.799
LGA    F     303      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)   16   90    5.0     12    2.63     0.00      9.801     0.439

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.265546 * X  +   0.678035 * Y  +   0.685386 * Z  +  41.292805
  Y_new =   0.952093 * X  +  -0.296270 * Y  +  -0.075786 * Z  +  25.377161
  Z_new =   0.151674 * X  +   0.672675 * Y  +  -0.724226 * Z  +   2.631708 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.393081   -0.748512  [ DEG:   137.1134    -42.8866 ]
  Theta =  -0.152261   -2.989331  [ DEG:    -8.7239   -171.2761 ]
  Phi   =   1.298801   -1.842791  [ DEG:    74.4158   -105.5842 ]
 
# 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: T0316TS307_5u-D3                              
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS307_5u-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   16   90   5.0   12   2.63    0.00   9.801
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS307_5u-D3
PFRMAT   TS
TARGET   T0316
MODEL    5  UNREFINED
PARENT   1xng_A
ATOM   1868  N   MET   284      23.612  23.099   0.159  1.00 21.65           N  
ATOM   1869  CA  MET   284      22.964  22.178  -0.772  1.00 22.93           C  
ATOM   1870  C   MET   284      23.537  22.256  -2.180  1.00 23.71           C  
ATOM   1871  O   MET   284      23.608  21.249  -2.886  1.00 25.42           O  
ATOM   1877  N   SER   285      23.945  23.451  -2.589  1.00 23.27           N  
ATOM   1878  CA  SER   285      24.510  23.646  -3.916  1.00 25.22           C  
ATOM   1879  C   SER   285      25.884  23.003  -4.071  1.00 24.93           C  
ATOM   1880  O   SER   285      26.265  22.589  -5.166  1.00 25.81           O  
ATOM   1886  N   THR   286      26.625  22.916  -2.974  1.00 22.65           N  
ATOM   1887  CA  THR   286      27.969  22.361  -3.032  1.00 22.35           C  
ATOM   1888  C   THR   286      28.166  21.010  -2.352  1.00 22.20           C  
ATOM   1889  O   THR   286      29.300  20.575  -2.161  1.00 21.75           O  
ATOM   1894  N   SER   287      27.075  20.333  -2.003  1.00 22.27           N  
ATOM   1895  CA  SER   287      27.185  19.039  -1.333  1.00 21.44           C  
ATOM   1896  C   SER   287      28.001  18.031  -2.145  1.00 21.10           C  
ATOM   1897  O   SER   287      28.639  17.138  -1.582  1.00 20.88           O  
ATOM   1899  N   LEU   288      27.989  18.193  -3.464  1.00 21.94           N  
ATOM   1900  CA  LEU   288      28.710  17.299  -4.368  1.00 21.80           C  
ATOM   1901  C   LEU   288      30.222  17.278  -4.167  1.00 21.06           C  
ATOM   1902  O   LEU   288      30.880  16.300  -4.519  1.00 21.74           O  
ATOM   1910  N   GLU   289      30.783  18.354  -3.623  1.00 20.72           N  
ATOM   1911  CA  GLU   289      32.228  18.416  -3.417  1.00 20.40           C  
ATOM   1912  C   GLU   289      32.718  17.484  -2.317  1.00 22.27           C  
ATOM   1913  O   GLU   289      33.913  17.207  -2.220  1.00 22.11           O  
ATOM   1919  N   HIS   294      31.789  16.992  -1.501  1.00 24.15           N  
ATOM   1920  CA  HIS   294      32.110  16.097  -0.389  1.00 26.32           C  
ATOM   1921  C   HIS   294      31.791  14.652  -0.756  1.00 28.08           C  
ATOM   1922  O   HIS   294      31.871  13.747   0.083  1.00 28.88           O  
ATOM   1927  N   PHE   295      31.435  14.443  -2.017  1.00 26.69           N  
ATOM   1928  CA  PHE   295      31.068  13.122  -2.496  1.00 29.32           C  
ATOM   1929  C   PHE   295      31.942  12.672  -3.655  1.00 27.54           C  
ATOM   1930  O   PHE   295      32.606  13.482  -4.302  1.00 26.74           O  
ATOM   1936  N   THR   296      31.947  11.366  -3.899  1.00 27.95           N  
ATOM   1937  CA  THR   296      32.702  10.789  -5.002  1.00 27.22           C  
ATOM   1938  C   THR   296      31.868  10.972  -6.270  1.00 25.81           C  
ATOM   1939  O   THR   296      30.650  11.141  -6.199  1.00 28.08           O  
ATOM   1944  N   ARG   297      32.511  10.952  -7.447  1.00 26.18           N  
ATOM   1945  CA  ARG   297      31.761  11.116  -8.695  1.00 25.53           C  
ATOM   1946  C   ARG   297      30.791   9.957  -8.894  1.00 25.64           C  
ATOM   1947  O   ARG   297      31.050   8.837  -8.441  1.00 26.59           O  
ATOM   1951  N   GLU   298      29.670  10.239  -9.549  1.00 24.57           N  
ATOM   1952  CA  GLU   298      28.649   9.233  -9.818  1.00 24.88           C  
ATOM   1953  C   GLU   298      29.133   8.291 -10.914  1.00 24.28           C  
ATOM   1954  O   GLU   298      29.449   8.735 -12.017  1.00 23.34           O  
ATOM   1956  N   MET   299      29.184   6.999 -10.607  1.00 24.24           N  
ATOM   1957  CA  MET   299      29.624   5.991 -11.569  1.00 24.38           C  
ATOM   1958  C   MET   299      28.481   5.015 -11.830  1.00 24.52           C  
ATOM   1959  O   MET   299      27.881   4.491 -10.892  1.00 25.79           O  
ATOM   1964  N   PRO   300      28.182   4.770 -13.099  1.00 25.46           N  
ATOM   1965  CA  PRO   300      27.111   3.847 -13.455  1.00 26.01           C  
ATOM   1966  C   PRO   300      27.427   2.456 -12.910  1.00 26.81           C  
ATOM   1967  O   PRO   300      28.513   1.929 -13.141  1.00 26.71           O  
ATOM   1969  N   GLU   301      26.483   1.871 -12.179  1.00 26.18           N  
ATOM   1970  CA  GLU   301      26.680   0.541 -11.610  1.00 27.84           C  
ATOM   1971  C   GLU   301      26.902  -0.488 -12.715  1.00 28.66           C  
ATOM   1972  O   GLU   301      26.426  -0.322 -13.839  1.00 26.57           O  
ATOM   1974  N   GLU   302      27.630  -1.552 -12.392  1.00 29.84           N  
ATOM   1975  CA  GLU   302      27.908  -2.592 -13.372  1.00 32.53           C  
ATOM   1976  C   GLU   302      26.602  -3.191 -13.887  1.00 33.67           C  
ATOM   1977  O   GLU   302      25.787  -3.689 -13.108  1.00 33.88           O  
ATOM   1985  N   PHE   303      26.411  -3.127 -15.202  1.00 35.27           N  
ATOM   1986  CA  PHE   303      25.211  -3.651 -15.851  1.00 37.06           C  
ATOM   1987  C   PHE   303      25.071  -5.150 -15.622  1.00 37.32           C  
ATOM   1988  O   PHE   303      25.837  -5.937 -16.176  1.00 38.58           O  
TER
END
