
#######################################################
#                                                     #
#                        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 T0356TS213_1_3-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected  192 , name T0356_D2.pdb
# PARAMETERS: T0356TS213_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    -       -      V     165           -
LGA    -       -      T     166           -
LGA    -       -      R     167           -
LGA    -       -      G     168           -
LGA    -       -      P     169           -
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    T     122      R     192          1.220
LGA    K     123      W     193          1.443
LGA    R     124      L     194          3.370
LGA    -       -      S     195           -
LGA    -       -      H     196           -
LGA    -       -      R     197           -
LGA    -       -      G     198           -
LGA    -       -      G     199           -
LGA    L     125      A     200          2.034
LGA    R     126      L     201          2.308
LGA    G     127      D     202          2.030
LGA    A     128      Y     203          2.148
LGA    -       -      Q     204           -
LGA    -       -      E     205           -
LGA    P     129      W     206          0.819
LGA    C     130      C     207          1.001
LGA    Q     131      A     208          1.656
LGA    -       -      A     209           -
LGA    -       -      H     210           -
LGA    -       -      P     211           -
LGA    -       -      G     212           -
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    1.94    10.00      4.742     0.491

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.647687 * X  +  -0.451544 * Y  +  -0.613686 * Z  +  85.100601
  Y_new =   0.745674 * X  +   0.541053 * Y  +   0.388886 * Z  +  40.491730
  Z_new =   0.156437 * X  +  -0.709486 * Y  +   0.687137 * Z  +  77.403664 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.801398    2.340194  [ DEG:   -45.9167    134.0833 ]
  Theta =  -0.157082   -2.984510  [ DEG:    -9.0002   -170.9998 ]
  Phi   =   0.855607   -2.285986  [ DEG:    49.0227   -130.9773 ]
 
# 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: T0356TS213_1_3-D2                             
REMARK     2: T0356_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS213_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   1.94   10.00   4.742
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS213_1_3-D2
REMARK PARENT number 3
PFRMAT TS
TARGET T0356
PARENT 1r8j_A
ATOM    959  N   THR   122      70.906  52.600  82.066  1.00108.26       1SG 960
ATOM    960  CA  THR   122      70.526  52.004  80.820  1.00108.26       1SG 961
ATOM    961  CB  THR   122      69.094  51.549  80.774  1.00108.26       1SG 962
ATOM    962  OG1 THR   122      68.816  50.918  79.532  1.00108.26       1SG 963
ATOM    963  CG2 THR   122      68.163  52.755  80.991  1.00108.26       1SG 964
ATOM    964  C   THR   122      70.723  53.049  79.771  1.00108.26       1SG 965
ATOM    965  O   THR   122      70.236  54.171  79.891  1.00108.26       1SG 966
ATOM    966  N   LYS   123      71.485  52.720  78.713  1.00 68.78       1SG 967
ATOM    967  CA  LYS   123      71.708  53.706  77.699  1.00 68.78       1SG 968
ATOM    968  CB  LYS   123      72.975  54.552  77.923  1.00 68.78       1SG 969
ATOM    969  CG  LYS   123      72.912  55.424  79.178  1.00 68.78       1SG 970
ATOM    970  CD  LYS   123      74.275  55.979  79.598  1.00 68.78       1SG 971
ATOM    971  CE  LYS   123      74.232  56.854  80.852  1.00 68.78       1SG 972
ATOM    972  NZ  LYS   123      75.599  57.303  81.203  1.00 68.78       1SG 973
ATOM    973  C   LYS   123      71.882  52.984  76.409  1.00 68.78       1SG 974
ATOM    974  O   LYS   123      71.890  51.754  76.362  1.00 68.78       1SG 975
ATOM    975  N   ARG   124      71.986  53.760  75.315  1.00122.16       1SG 976
ATOM    976  CA  ARG   124      72.201  53.206  74.012  1.00122.16       1SG 977
ATOM    977  CB  ARG   124      71.894  54.175  72.860  1.00122.16       1SG 978
ATOM    978  CG  ARG   124      70.411  54.309  72.517  1.00122.16       1SG 979
ATOM    979  CD  ARG   124      69.536  54.894  73.625  1.00122.16       1SG 980
ATOM    980  NE  ARG   124      68.177  55.065  73.041  1.00122.16       1SG 981
ATOM    981  CZ  ARG   124      67.344  53.987  72.962  1.00122.16       1SG 982
ATOM    982  NH1 ARG   124      67.758  52.777  73.437  1.00122.16       1SG 983
ATOM    983  NH2 ARG   124      66.111  54.113  72.388  1.00122.16       1SG 984
ATOM    984  C   ARG   124      73.646  52.853  73.896  1.00122.16       1SG 985
ATOM    985  O   ARG   124      74.485  53.399  74.611  1.00122.16       1SG 986
ATOM    986  N   LEU   125      73.971  51.918  72.982  1.00 76.19       1SG 987
ATOM    987  CA  LEU   125      75.331  51.500  72.825  1.00 76.19       1SG 988
ATOM    988  CB  LEU   125      75.515  50.310  71.864  1.00 76.19       1SG 989
ATOM    989  CG  LEU   125      76.985  49.873  71.703  1.00 76.19       1SG 990
ATOM    990  CD1 LEU   125      77.576  49.390  73.039  1.00 76.19       1SG 991
ATOM    991  CD2 LEU   125      77.145  48.845  70.570  1.00 76.19       1SG 992
ATOM    992  C   LEU   125      76.110  52.644  72.272  1.00 76.19       1SG 993
ATOM    993  O   LEU   125      75.636  53.396  71.420  1.00 76.19       1SG 994
ATOM    994  N   ARG   126      77.343  52.808  72.777  1.00176.40       1SG 995
ATOM    995  CA  ARG   126      78.213  53.836  72.300  1.00176.40       1SG 996
ATOM    996  CB  ARG   126      78.816  54.712  73.413  1.00176.40       1SG 997
ATOM    997  CG  ARG   126      77.785  55.464  74.253  1.00176.40       1SG 998
ATOM    998  CD  ARG   126      78.409  56.396  75.292  1.00176.40       1SG 999
ATOM    999  NE  ARG   126      78.538  57.740  74.662  1.00176.40       1SG1000
ATOM   1000  CZ  ARG   126      77.485  58.607  74.710  1.00176.40       1SG1001
ATOM   1001  NH1 ARG   126      76.335  58.250  75.349  1.00176.40       1SG1002
ATOM   1002  NH2 ARG   126      77.586  59.836  74.122  1.00176.40       1SG1003
ATOM   1003  C   ARG   126      79.350  53.098  71.691  1.00176.40       1SG1004
ATOM   1004  O   ARG   126      79.490  51.893  71.894  1.00176.40       1SG1005
ATOM   1005  N   GLY   127      80.179  53.787  70.890  1.00 23.35       1SG1006
ATOM   1006  CA  GLY   127      81.295  53.075  70.354  1.00 23.35       1SG1007
ATOM   1007  C   GLY   127      82.101  52.666  71.540  1.00 23.35       1SG1008
ATOM   1008  O   GLY   127      82.372  53.476  72.425  1.00 23.35       1SG1009
ATOM   1009  N   ALA   128      82.515  51.388  71.583  1.00 32.69       1SG1010
ATOM   1010  CA  ALA   128      83.249  50.943  72.727  1.00 32.69       1SG1011
ATOM   1011  CB  ALA   128      82.819  49.559  73.241  1.00 32.69       1SG1012
ATOM   1012  C   ALA   128      84.674  50.845  72.326  1.00 32.69       1SG1013
ATOM   1013  O   ALA   128      85.013  50.399  71.231  1.00 32.69       1SG1014
ATOM   1014  N   PRO   129      85.508  51.318  73.205  1.00128.81       1SG1015
ATOM   1015  CA  PRO   129      86.924  51.263  73.011  1.00128.81       1SG1016
ATOM   1016  CD  PRO   129      85.124  52.315  74.187  1.00128.81       1SG1017
ATOM   1017  CB  PRO   129      87.538  52.188  74.065  1.00128.81       1SG1018
ATOM   1018  CG  PRO   129      86.387  52.478  75.046  1.00128.81       1SG1019
ATOM   1019  C   PRO   129      87.368  49.846  73.105  1.00128.81       1SG1020
ATOM   1020  O   PRO   129      88.438  49.516  72.599  1.00128.81       1SG1021
ATOM   1021  N   CYS   130      86.572  48.988  73.767  1.00 22.38       1SG1022
ATOM   1022  CA  CYS   130      86.972  47.619  73.846  1.00 22.38       1SG1023
ATOM   1023  CB  CYS   130      85.956  46.745  74.604  1.00 22.38       1SG1024
ATOM   1024  SG  CYS   130      85.882  47.114  76.384  1.00 22.38       1SG1025
ATOM   1025  C   CYS   130      87.018  47.125  72.438  1.00 22.38       1SG1026
ATOM   1026  O   CYS   130      87.970  46.465  72.024  1.00 22.38       1SG1027
ATOM   1027  N   GLN   131      85.982  47.487  71.663  1.00 75.87       1SG1028
ATOM   1028  CA  GLN   131      85.831  47.088  70.294  1.00 75.87       1SG1029
ATOM   1029  CB  GLN   131      86.713  47.870  69.304  1.00 75.87       1SG1030
ATOM   1030  CG  GLN   131      88.210  47.592  69.462  1.00 75.87       1SG1031
ATOM   1031  CD  GLN   131      88.954  48.411  68.418  1.00 75.87       1SG1032
ATOM   1032  OE1 GLN   131      89.701  47.873  67.601  1.00 75.87       1SG1033
ATOM   1033  NE2 GLN   131      88.749  49.755  68.447  1.00 75.87       1SG1034
ATOM   1034  C   GLN   131      86.158  45.607  70.155  1.00 75.87       1SG1035
ATOM   1035  O   GLN   131      86.473  45.193  69.008  1.00 75.87       1SG1036
ATOM   1036  OXT GLN   131      86.090  44.871  71.176  1.00 75.87       1SG1037
TER
END
