
#######################################################
#                                                     #
#                        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   10 (   78),  selected   10 , name T0356TS418_1_3-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected  192 , name T0356_D2.pdb
# PARAMETERS: T0356TS418_1_3-D2.T0356_D2.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    -       -      T     122           -
LGA    -       -      K     123           -
LGA    -       -      R     124           -
LGA    -       -      L     125           -
LGA    -       -      R     126           -
LGA    -       -      G     127           -
LGA    -       -      A     128           -
LGA    -       -      P     129           -
LGA    -       -      C     130           -
LGA    -       -      Q     131           -
LGA    -       -      Q     132           -
LGA    -       -      K     133           -
LGA    -       -      I     134           -
LGA    -       -      V     135           -
LGA    -       -      S     136           -
LGA    -       -      G     137           -
LGA    -       -      D     138           -
LGA    -       -      D     139           -
LGA    -       -      V     140           -
LGA    -       -      D     141           -
LGA    -       -      L     142           -
LGA    -       -      N     143           -
LGA    -       -      R     144           -
LGA    -       -      I     145           -
LGA    -       -      P     146           -
LGA    -       -      I     147           -
LGA    -       -      M     148           -
LGA    -       -      T     149           -
LGA    -       -      C     150           -
LGA    -       -      W     151           -
LGA    -       -      P     152           -
LGA    -       -      E     153           -
LGA    -       -      D     154           -
LGA    -       -      A     155           -
LGA    -       -      A     156           -
LGA    -       -      P     157           -
LGA    -       -      L     158           -
LGA    -       -      I     159           -
LGA    -       -      T     160           -
LGA    -       -      W     161           -
LGA    -       -      G     162           -
LGA    -       -      L     163           -
LGA    -       -      T     164           -
LGA    T     122      V     165          0.849
LGA    K     123      T     166          0.749
LGA    R     124      R     167          1.343
LGA    L     125      G     168          0.914
LGA    R     126      P     169          1.681
LGA    -       -      H     170           -
LGA    -       -      K     171           -
LGA    -       -      E     172           -
LGA    -       -      R     173           -
LGA    -       -      Q     174           -
LGA    -       -      N     175           -
LGA    -       -      L     176           -
LGA    -       -      G     177           -
LGA    -       -      I     178           -
LGA    -       -      Y     179           -
LGA    -       -      R     180           -
LGA    -       -      Q     181           -
LGA    -       -      Q     182           -
LGA    -       -      L     183           -
LGA    -       -      I     184           -
LGA    -       -      G     185           -
LGA    -       -      K     186           -
LGA    -       -      N     187           -
LGA    -       -      K     188           -
LGA    -       -      L     189           -
LGA    -       -      I     190           -
LGA    -       -      M     191           -
LGA    -       -      R     192           -
LGA    -       -      W     193           -
LGA    -       -      L     194           -
LGA    -       -      S     195           -
LGA    -       -      H     196           -
LGA    -       -      R     197           -
LGA    -       -      G     198           -
LGA    -       -      G     199           -
LGA    -       -      A     200           -
LGA    -       -      L     201           -
LGA    -       -      D     202           -
LGA    -       -      Y     203           -
LGA    -       -      Q     204           -
LGA    -       -      E     205           -
LGA    G     127      W     206          0.802
LGA    A     128      C     207          2.929
LGA    P     129      A     208          2.092
LGA    -       -      A     209           -
LGA    -       -      H     210           -
LGA    C     130      P     211          1.109
LGA    Q     131      G     212          2.781
LGA    -       -      E     213           -
LGA    -       -      R     214           -
LGA    -       -      F     215           -
LGA    -       -      P     216           -
LGA    -       -      V     217           -
LGA    -       -      S     218           -
LGA    -       -      V     219           -
LGA    -       -      A     220           -
LGA    -       -      L     221           -
LGA    -       -      G     222           -
LGA    -       -      A     223           -
LGA    -       -      D     224           -
LGA    -       -      P     225           -
LGA    -       -      A     226           -
LGA    -       -      T     227           -
LGA    -       -      I     228           -
LGA    -       -      L     229           -
LGA    -       -      G     230           -
LGA    -       -      A     231           -
LGA    -       -      V     232           -
LGA    -       -      T     233           -
LGA    -       -      P     234           -
LGA    -       -      V     235           -
LGA    -       -      P     236           -
LGA    -       -      D     237           -
LGA    -       -      T     238           -
LGA    -       -      L     239           -
LGA    -       -      S     240           -
LGA    -       -      E     241           -
LGA    -       -      Y     242           -
LGA    -       -      A     243           -
LGA    -       -      F     244           -
LGA    -       -      A     245           -
LGA    -       -      G     246           -
LGA    -       -      L     247           -
LGA    -       -      L     248           -
LGA    -       -      R     249           -
LGA    -       -      G     250           -
LGA    -       -      T     251           -
LGA    -       -      K     252           -
LGA    -       -      T     253           -
LGA    -       -      E     254           -
LGA    -       -      V     255           -
LGA    -       -      V     256           -
LGA    -       -      K     257           -
LGA    -       -      C     258           -
LGA    -       -      I     259           -
LGA    -       -      S     260           -
LGA    -       -      N     261           -
LGA    -       -      D     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      V     265           -
LGA    -       -      P     266           -
LGA    -       -      A     267           -
LGA    -       -      S     268           -
LGA    -       -      A     269           -
LGA    -       -      E     270           -
LGA    -       -      I     271           -
LGA    -       -      V     272           -
LGA    -       -      L     273           -
LGA    -       -      E     274           -
LGA    -       -      G     275           -
LGA    -       -      Y     276           -
LGA    -       -      I     277           -
LGA    -       -      E     278           -
LGA    -       -      Q     279           -
LGA    -       -      G     280           -
LGA    -       -      E     281           -
LGA    -       -      T     282           -
LGA    -       -      A     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      G     286           -
LGA    -       -      P     287           -
LGA    -       -      Y     288           -
LGA    -       -      G     289           -
LGA    -       -      D     290           -
LGA    -       -      H     291           -
LGA    -       -      T     292           -
LGA    -       -      G     293           -
LGA    -       -      Y     294           -
LGA    -       -      Y     295           -
LGA    -       -      N     296           -
LGA    -       -      E     297           -
LGA    -       -      V     298           -
LGA    -       -      D     299           -
LGA    -       -      S     300           -
LGA    -       -      F     301           -
LGA    -       -      P     302           -
LGA    -       -      V     303           -
LGA    -       -      F     304           -
LGA    -       -      T     305           -
LGA    -       -      V     306           -
LGA    -       -      T     307           -
LGA    -       -      H     308           -
LGA    -       -      I     309           -
LGA    -       -      T     310           -
LGA    -       -      Q     311           -
LGA    -       -      R     312           -
LGA    -       -      E     313           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   10  192    5.0     10    1.71    10.00      4.779     0.552

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.248569 * X  +   0.952545 * Y  +  -0.175701 * Z  +  74.910988
  Y_new =  -0.594216 * X  +   0.293210 * Y  +   0.748956 * Z  +  47.476479
  Z_new =   0.764932 * X  +  -0.081762 * Y  +   0.638901 * Z  +  68.834206 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.127282    3.014311  [ DEG:    -7.2927    172.7073 ]
  Theta =  -0.870936   -2.270657  [ DEG:   -49.9009   -130.0991 ]
  Phi   =  -1.174603    1.966990  [ DEG:   -67.2998    112.7002 ]
 
# 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: T0356TS418_1_3-D2                             
REMARK     2: T0356_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS418_1_3-D2.T0356_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   10  192   5.0   10   1.71   10.00   4.779
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS418_1_3-D2
REMARK PARENT number 3
PFRMAT TS
TARGET T0356
PARENT 1r8j_A
ATOM    959  N   THR   122      80.617  61.519  79.206  1.00108.94       1SG 960
ATOM    960  CA  THR   122      81.094  61.805  77.887  1.00108.94       1SG 961
ATOM    961  CB  THR   122      82.162  62.858  77.848  1.00108.94       1SG 962
ATOM    962  OG1 THR   122      82.421  63.246  76.508  1.00108.94       1SG 963
ATOM    963  CG2 THR   122      83.438  62.293  78.496  1.00108.94       1SG 964
ATOM    964  C   THR   122      81.688  60.532  77.381  1.00108.94       1SG 965
ATOM    965  O   THR   122      82.175  59.712  78.159  1.00108.94       1SG 966
ATOM    966  N   LYS   123      81.657  60.323  76.053  1.00104.18       1SG 967
ATOM    967  CA  LYS   123      82.130  59.068  75.547  1.00104.18       1SG 968
ATOM    968  CB  LYS   123      81.130  58.374  74.605  1.00104.18       1SG 969
ATOM    969  CG  LYS   123      79.785  58.032  75.250  1.00104.18       1SG 970
ATOM    970  CD  LYS   123      78.701  57.693  74.222  1.00104.18       1SG 971
ATOM    971  CE  LYS   123      78.223  58.906  73.420  1.00104.18       1SG 972
ATOM    972  NZ  LYS   123      77.436  58.466  72.244  1.00104.18       1SG 973
ATOM    973  C   LYS   123      83.363  59.293  74.741  1.00104.18       1SG 974
ATOM    974  O   LYS   123      83.534  60.335  74.111  1.00104.18       1SG 975
ATOM    975  N   ARG   124      84.273  58.300  74.780  1.00141.86       1SG 976
ATOM    976  CA  ARG   124      85.456  58.326  73.974  1.00141.86       1SG 977
ATOM    977  CB  ARG   124      86.628  57.517  74.550  1.00141.86       1SG 978
ATOM    978  CG  ARG   124      87.872  57.561  73.660  1.00141.86       1SG 979
ATOM    979  CD  ARG   124      89.159  57.139  74.368  1.00141.86       1SG 980
ATOM    980  NE  ARG   124      88.823  56.037  75.311  1.00141.86       1SG 981
ATOM    981  CZ  ARG   124      88.537  56.328  76.615  1.00141.86       1SG 982
ATOM    982  NH1 ARG   124      88.563  57.622  77.041  1.00141.86       1SG 983
ATOM    983  NH2 ARG   124      88.230  55.325  77.490  1.00141.86       1SG 984
ATOM    984  C   ARG   124      85.077  57.729  72.660  1.00141.86       1SG 985
ATOM    985  O   ARG   124      84.168  56.906  72.582  1.00141.86       1SG 986
ATOM    986  N   LEU   125      85.758  58.151  71.581  1.00158.91       1SG 987
ATOM    987  CA  LEU   125      85.383  57.706  70.272  1.00158.91       1SG 988
ATOM    988  CB  LEU   125      86.172  58.408  69.155  1.00158.91       1SG 989
ATOM    989  CG  LEU   125      85.700  58.018  67.743  1.00158.91       1SG 990
ATOM    990  CD1 LEU   125      84.246  58.460  67.506  1.00158.91       1SG 991
ATOM    991  CD2 LEU   125      86.658  58.544  66.661  1.00158.91       1SG 992
ATOM    992  C   LEU   125      85.592  56.228  70.120  1.00158.91       1SG 993
ATOM    993  O   LEU   125      84.708  55.525  69.632  1.00158.91       1SG 994
ATOM    994  N   ARG   126      86.749  55.692  70.555  1.00201.26       1SG 995
ATOM    995  CA  ARG   126      86.969  54.297  70.293  1.00201.26       1SG 996
ATOM    996  CB  ARG   126      88.327  53.990  69.643  1.00201.26       1SG 997
ATOM    997  CG  ARG   126      88.497  54.491  68.208  1.00201.26       1SG 998
ATOM    998  CD  ARG   126      88.447  56.011  68.064  1.00201.26       1SG 999
ATOM    999  NE  ARG   126      88.989  56.340  66.714  1.00201.26       1SG1000
ATOM   1000  CZ  ARG   126      88.206  56.231  65.607  1.00201.26       1SG1001
ATOM   1001  NH1 ARG   126      86.916  55.787  65.729  1.00201.26       1SG1002
ATOM   1002  NH2 ARG   126      88.700  56.550  64.377  1.00201.26       1SG1003
ATOM   1003  C   ARG   126      86.967  53.530  71.569  1.00201.26       1SG1004
ATOM   1004  O   ARG   126      87.627  53.900  72.539  1.00201.26       1SG1005
ATOM   1005  N   GLY   127      86.204  52.421  71.594  1.00 20.25       1SG1006
ATOM   1006  CA  GLY   127      86.224  51.564  72.739  1.00 20.25       1SG1007
ATOM   1007  C   GLY   127      87.318  50.582  72.490  1.00 20.25       1SG1008
ATOM   1008  O   GLY   127      87.939  50.588  71.427  1.00 20.25       1SG1009
ATOM   1009  N   ALA   128      87.591  49.703  73.470  1.00 30.45       1SG1010
ATOM   1010  CA  ALA   128      88.611  48.726  73.242  1.00 30.45       1SG1011
ATOM   1011  CB  ALA   128      89.633  48.604  74.387  1.00 30.45       1SG1012
ATOM   1012  C   ALA   128      87.919  47.414  73.115  1.00 30.45       1SG1013
ATOM   1013  O   ALA   128      87.076  47.042  73.931  1.00 30.45       1SG1014
ATOM   1014  N   PRO   129      88.240  46.725  72.065  1.00 55.92       1SG1015
ATOM   1015  CA  PRO   129      87.652  45.436  71.858  1.00 55.92       1SG1016
ATOM   1016  CD  PRO   129      88.576  47.387  70.815  1.00 55.92       1SG1017
ATOM   1017  CB  PRO   129      88.012  45.049  70.428  1.00 55.92       1SG1018
ATOM   1018  CG  PRO   129      88.131  46.409  69.714  1.00 55.92       1SG1019
ATOM   1019  C   PRO   129      88.110  44.481  72.907  1.00 55.92       1SG1020
ATOM   1020  O   PRO   129      87.367  43.557  73.240  1.00 55.92       1SG1021
ATOM   1021  N   CYS   130      89.335  44.678  73.424  1.00 20.71       1SG1022
ATOM   1022  CA  CYS   130      89.852  43.832  74.455  1.00 20.71       1SG1023
ATOM   1023  CB  CYS   130      91.320  44.131  74.804  1.00 20.71       1SG1024
ATOM   1024  SG  CYS   130      92.438  43.760  73.422  1.00 20.71       1SG1025
ATOM   1025  C   CYS   130      89.026  44.069  75.675  1.00 20.71       1SG1026
ATOM   1026  O   CYS   130      88.738  43.144  76.432  1.00 20.71       1SG1027
ATOM   1027  N   GLN   131      88.615  45.338  75.875  1.00 71.49       1SG1028
ATOM   1028  CA  GLN   131      87.852  45.751  77.017  1.00 71.49       1SG1029
ATOM   1029  CB  GLN   131      86.370  45.314  76.976  1.00 71.49       1SG1030
ATOM   1030  CG  GLN   131      86.149  43.802  77.052  1.00 71.49       1SG1031
ATOM   1031  CD  GLN   131      84.653  43.529  77.042  1.00 71.49       1SG1032
ATOM   1032  OE1 GLN   131      83.872  44.281  76.459  1.00 71.49       1SG1033
ATOM   1033  NE2 GLN   131      84.235  42.418  77.705  1.00 71.49       1SG1034
ATOM   1034  C   GLN   131      88.523  45.194  78.269  1.00 71.49       1SG1035
ATOM   1035  O   GLN   131      89.748  45.444  78.424  1.00 71.49       1SG1036
ATOM   1036  OXT GLN   131      87.838  44.522  79.088  1.00 71.49       1SG1037
TER
END
