
#######################################################
#                                                     #
#                        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    5 (   44),  selected    5 , name T0338TS021_1-D2
# Molecule2: number of CA atoms  113 (  914),  selected  113 , name T0338_D2.pdb
# PARAMETERS: T0338TS021_1-D2.T0338_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    -       -      E     144           -
LGA    -       -      H     145           -
LGA    -       -      P     146           -
LGA    -       -      H     147           -
LGA    -       -      T     148           -
LGA    -       -      D     149           -
LGA    -       -      V     150           -
LGA    -       -      V     151           -
LGA    -       -      K     152           -
LGA    -       -      C     153           -
LGA    -       -      T     154           -
LGA    -       -      Q     155           -
LGA    -       -      L     156           -
LGA    -       -      V     157           -
LGA    -       -      R     158           -
LGA    -       -      A     159           -
LGA    -       -      S     160           -
LGA    -       -      K     161           -
LGA    -       -      D     162           -
LGA    -       -      L     163           -
LGA    -       -      A     164           -
LGA    -       -      Q     165           -
LGA    -       -      T     166           -
LGA    -       -      S     167           -
LGA    -       -      Y     168           -
LGA    -       -      F     169           -
LGA    -       -      M     170           -
LGA    -       -      A     171           -
LGA    -       -      T     172           -
LGA    -       -      N     173           -
LGA    -       -      S     174           -
LGA    -       -      L     175           -
LGA    -       -      H     176           -
LGA    -       -      L     177           -
LGA    -       -      T     178           -
LGA    -       -      T     179           -
LGA    -       -      F     180           -
LGA    -       -      C     181           -
LGA    -       -      L     182           -
LGA    -       -      Q     183           -
LGA    -       -      Y     184           -
LGA    -       -      K     185           -
LGA    -       -      P     186           -
LGA    -       -      T     187           -
LGA    -       -      V     188           -
LGA    -       -      I     189           -
LGA    -       -      A     190           -
LGA    -       -      C     191           -
LGA    -       -      V     192           -
LGA    -       -      C     193           -
LGA    -       -      I     194           -
LGA    -       -      H     195           -
LGA    -       -      L     196           -
LGA    -       -      A     197           -
LGA    -       -      C     198           -
LGA    -       -      K     199           -
LGA    -       -      W     200           -
LGA    -       -      S     201           -
LGA    -       -      N     202           -
LGA    -       -      W     203           -
LGA    -       -      E     204           -
LGA    -       -      I     205           -
LGA    -       -      P     206           -
LGA    -       -      V     207           -
LGA    -       -      S     208           -
LGA    -       -      T     209           -
LGA    -       -      D     210           -
LGA    -       -      G     211           -
LGA    -       -      K     212           -
LGA    -       -      H     213           -
LGA    -       -      W     214           -
LGA    -       -      W     215           -
LGA    -       -      E     216           -
LGA    -       -      Y     217           -
LGA    -       -      V     218           -
LGA    E     144      D     219          1.347
LGA    H     145      P     220          0.465
LGA    P     146      T     221          0.572
LGA    H     147      V     222          0.615
LGA    T     148      T     223          1.068
LGA    -       -      L     224           -
LGA    -       -      E     225           -
LGA    -       -      L     226           -
LGA    -       -      L     227           -
LGA    -       -      D     228           -
LGA    -       -      E     229           -
LGA    -       -      L     230           -
LGA    -       -      T     231           -
LGA    -       -      H     232           -
LGA    -       -      E     233           -
LGA    -       -      F     234           -
LGA    -       -      L     235           -
LGA    -       -      Q     236           -
LGA    -       -      I     237           -
LGA    -       -      L     238           -
LGA    -       -      E     239           -
LGA    -       -      K     240           -
LGA    -       -      T     241           -
LGA    -       -      P     242           -
LGA    -       -      N     243           -
LGA    -       -      R     244           -
LGA    -       -      L     245           -
LGA    -       -      K     246           -
LGA    -       -      K     247           -
LGA    -       -      I     248           -
LGA    -       -      R     249           -
LGA    -       -      N     250           -
LGA    -       -      W     251           -
LGA    -       -      R     252           -
LGA    -       -      A     253           -
LGA    -       -      N     254           -
LGA    -       -      Q     255           -
LGA    -       -      A     256           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5  113    5.0      5    0.88    20.00      4.355     0.510

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.337888 * X  +  -0.412720 * Y  +  -0.845868 * Z  + -27.203913
  Y_new =  -0.940562 * X  +   0.180797 * Y  +   0.287499 * Z  + -19.655840
  Z_new =   0.034274 * X  +   0.892734 * Y  +  -0.449278 * Z  +  46.265587 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.037049   -1.104543  [ DEG:   116.7143    -63.2857 ]
  Theta =  -0.034280   -3.107312  [ DEG:    -1.9641   -178.0359 ]
  Phi   =  -1.915680    1.225913  [ DEG:  -109.7604     70.2396 ]
 
# 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: T0338TS021_1-D2                               
REMARK     2: T0338_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0338TS021_1-D2.T0338_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5  113   5.0    5   0.88   20.00   4.355
REMARK  ---------------------------------------------------------- 
MOLECULE T0338TS021_1-D2
PFRMAT TS
TARGET T0338
MODEL 1
PARENT N/A
ATOM   1159  N   GLU   144     -27.910   5.570  67.265  1.00441.44       1SG1160
ATOM   1160  CA  GLU   144     -27.955   5.329  65.851  1.00441.44       1SG1161
ATOM   1161  CB  GLU   144     -26.686   5.683  65.053  1.00441.44       1SG1162
ATOM   1162  CG  GLU   144     -26.875   5.579  63.540  1.00441.44       1SG1163
ATOM   1163  CD  GLU   144     -27.738   6.752  63.100  1.00441.44       1SG1164
ATOM   1164  OE1 GLU   144     -28.152   7.549  63.986  1.00441.44       1SG1165
ATOM   1165  OE2 GLU   144     -27.996   6.868  61.872  1.00441.44       1SG1166
ATOM   1166  C   GLU   144     -28.193   3.872  65.696  1.00441.44       1SG1167
ATOM   1167  O   GLU   144     -27.716   3.073  66.499  1.00441.44       1SG1168
ATOM   1168  N   HIS   145     -28.953   3.479  64.661  1.00149.75       1SG1169
ATOM   1169  CA  HIS   145     -29.156   2.076  64.497  1.00149.75       1SG1170
ATOM   1170  ND1 HIS   145     -29.144  -0.277  62.092  1.00149.75       1SG1171
ATOM   1171  CG  HIS   145     -30.011   0.236  63.031  1.00149.75       1SG1172
ATOM   1172  CB  HIS   145     -30.103   1.697  63.345  1.00149.75       1SG1173
ATOM   1173  NE2 HIS   145     -30.221  -2.008  62.974  1.00149.75       1SG1174
ATOM   1174  CD2 HIS   145     -30.661  -0.834  63.560  1.00149.75       1SG1175
ATOM   1175  CE1 HIS   145     -29.310  -1.624  62.100  1.00149.75       1SG1176
ATOM   1176  C   HIS   145     -27.828   1.460  64.249  1.00149.75       1SG1177
ATOM   1177  O   HIS   145     -27.473   0.443  64.842  1.00149.75       1SG1178
ATOM   1178  N   PRO   146     -27.055   2.036  63.394  1.00134.43       1SG1179
ATOM   1179  CA  PRO   146     -25.758   1.492  63.198  1.00134.43       1SG1180
ATOM   1180  CD  PRO   146     -27.520   2.774  62.230  1.00134.43       1SG1181
ATOM   1181  CB  PRO   146     -25.260   2.023  61.850  1.00134.43       1SG1182
ATOM   1182  CG  PRO   146     -26.226   3.170  61.504  1.00134.43       1SG1183
ATOM   1183  C   PRO   146     -24.908   1.874  64.375  1.00134.43       1SG1184
ATOM   1184  O   PRO   146     -23.768   1.430  64.443  1.00134.43       1SG1185
ATOM   1185  N   HIS   147     -25.399   2.715  65.309  1.00116.07       1SG1186
ATOM   1186  CA  HIS   147     -24.532   3.084  66.397  1.00116.07       1SG1187
ATOM   1187  ND1 HIS   147     -23.557   4.879  69.158  1.00116.07       1SG1188
ATOM   1188  CG  HIS   147     -23.625   5.004  67.789  1.00116.07       1SG1189
ATOM   1189  CB  HIS   147     -24.758   4.507  66.939  1.00116.07       1SG1190
ATOM   1190  NE2 HIS   147     -21.705   5.933  68.526  1.00116.07       1SG1191
ATOM   1191  CD2 HIS   147     -22.484   5.650  67.419  1.00116.07       1SG1192
ATOM   1192  CE1 HIS   147     -22.390   5.452  69.546  1.00116.07       1SG1193
ATOM   1193  C   HIS   147     -24.722   2.126  67.535  1.00116.07       1SG1194
ATOM   1194  O   HIS   147     -25.653   1.323  67.533  1.00116.07       1SG1195
ATOM   1195  N   THR   148     -23.793   2.166  68.518  1.00147.19       1SG1196
ATOM   1196  CA  THR   148     -23.826   1.339  69.689  1.00147.19       1SG1197
ATOM   1197  CB  THR   148     -23.496  -0.097  69.428  1.00147.19       1SG1198
ATOM   1198  OG1 THR   148     -23.775  -0.883  70.578  1.00147.19       1SG1199
ATOM   1199  CG2 THR   148     -22.004  -0.198  69.069  1.00147.19       1SG1200
ATOM   1200  C   THR   148     -22.704   1.830  70.597  1.00147.19       1SG1201
ATOM   1201  O   THR   148     -22.602   1.292  71.735  1.00147.19       1SG1202
ATOM   1202  OXT THR   148     -21.937   2.733  70.172  1.00147.19       1SG1203
TER
END
