
#######################################################
#                                                     #
#                        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    9 (   75),  selected    9 , name T0372TS671_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS671_2-D1.T0372_D1.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       1           -
LGA    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    K     290      L      77          1.222
LGA    Y     291      R      78          1.739
LGA    M     292      K      79          1.883
LGA    A     293      L      80          3.165
LGA    C     294      I      81          1.585
LGA    -       -      E      82           -
LGA    -       -      D      83           -
LGA    L     295      A      84          0.637
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    K     296      H      89          1.557
LGA    D     297      N      90          0.646
LGA    H     298      F      91          0.810
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    9  126    5.0      9    1.65     0.00      6.666     0.514

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.127921 * X  +   0.006778 * Y  +  -0.991761 * Z  +  68.820526
  Y_new =   0.221148 * X  +   0.974995 * Y  +  -0.021861 * Z  +  10.050424
  Z_new =   0.966814 * X  +  -0.222122 * Y  +  -0.126221 * Z  + -29.413393 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.087544    1.054049  [ DEG:  -119.6074     60.3926 ]
  Theta =  -1.312452   -1.829140  [ DEG:   -75.1980   -104.8020 ]
  Phi   =   2.095212   -1.046381  [ DEG:   120.0468    -59.9532 ]
 
# 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: T0372TS671_2-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS671_2-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    9  126   5.0    9   1.65    0.00   6.666
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS671_2-D1
PFRMAT TS
TARGET T0372
MODEL  2  REFINED
PARENT 2GE3_A 1YR0_D 1YVO_B
ATOM   1097  N   LYS   290      31.993  57.998  -5.071  1.00  0.00
ATOM   1098  CA  LYS   290      31.947  57.223  -6.324  1.00  0.00
ATOM   1099  C   LYS   290      32.669  57.930  -7.547  1.00  0.00
ATOM   1100  O   LYS   290      32.614  57.437  -8.688  1.00  0.00
ATOM   1101  CB  LYS   290      30.458  56.954  -6.633  1.00  0.00
ATOM   1102  CG  LYS   290      29.767  56.086  -5.557  1.00  0.00
ATOM   1103  CD  LYS   290      28.297  55.848  -5.759  1.00  0.00
ATOM   1104  CE  LYS   290      27.778  54.580  -5.157  1.00  0.00
ATOM   1105  NZ  LYS   290      26.299  54.501  -5.142  1.00  0.00
ATOM   1106  N   TYR   291      33.568  58.798  -7.207  1.00  0.00
ATOM   1107  CA  TYR   291      34.433  59.498  -8.134  1.00  0.00
ATOM   1108  C   TYR   291      35.749  58.719  -8.144  1.00  0.00
ATOM   1109  O   TYR   291      36.611  59.130  -8.953  1.00  0.00
ATOM   1110  CB  TYR   291      34.590  60.970  -7.735  1.00  0.00
ATOM   1111  CG  TYR   291      35.117  61.824  -8.855  1.00  0.00
ATOM   1112  CD1 TYR   291      36.469  62.001  -9.019  1.00  0.00
ATOM   1113  CD2 TYR   291      34.243  62.432  -9.724  1.00  0.00
ATOM   1114  CE1 TYR   291      36.949  62.757 -10.050  1.00  0.00
ATOM   1115  CE2 TYR   291      34.723  63.193 -10.773  1.00  0.00
ATOM   1116  CZ  TYR   291      36.081  63.350 -10.930  1.00  0.00
ATOM   1117  OH  TYR   291      36.612  64.049 -12.013  1.00  0.00
ATOM   1118  N   MET   292      36.143  58.208  -6.943  1.00  0.00
ATOM   1119  CA  MET   292      37.302  57.388  -6.937  1.00  0.00
ATOM   1120  C   MET   292      36.754  56.131  -7.609  1.00  0.00
ATOM   1121  O   MET   292      35.759  55.527  -7.216  1.00  0.00
ATOM   1122  CB  MET   292      37.792  57.025  -5.577  1.00  0.00
ATOM   1123  CG  MET   292      38.936  56.054  -5.554  1.00  0.00
ATOM   1124  SD  MET   292      40.512  56.982  -5.645  1.00  0.00
ATOM   1125  CE  MET   292      41.018  56.484  -7.280  1.00  0.00
ATOM   1126  N   ALA   293      36.978  56.227  -8.856  1.00  0.00
ATOM   1127  CA  ALA   293      36.526  55.451  -9.947  1.00  0.00
ATOM   1128  C   ALA   293      36.523  53.960  -9.703  1.00  0.00
ATOM   1129  O   ALA   293      37.005  53.437  -8.686  1.00  0.00
ATOM   1130  CB  ALA   293      37.459  55.793 -11.147  1.00  0.00
ATOM   1131  N   CYS   294      35.443  53.495 -10.244  1.00  0.00
ATOM   1132  CA  CYS   294      35.066  52.149 -10.342  1.00  0.00
ATOM   1133  C   CYS   294      36.146  51.303 -11.009  1.00  0.00
ATOM   1134  O   CYS   294      36.853  51.735 -11.946  1.00  0.00
ATOM   1135  CB  CYS   294      33.800  52.152 -11.173  1.00  0.00
ATOM   1136  SG  CYS   294      33.190  50.468 -11.309  1.00  0.00
ATOM   1137  N   LEU   295      36.527  50.331 -10.237  1.00  0.00
ATOM   1138  CA  LEU   295      37.458  49.310 -10.554  1.00  0.00
ATOM   1139  C   LEU   295      36.890  48.015  -9.901  1.00  0.00
ATOM   1140  O   LEU   295      36.822  47.931  -8.665  1.00  0.00
ATOM   1141  CB  LEU   295      38.850  49.606  -9.916  1.00  0.00
ATOM   1142  CG  LEU   295      40.086  48.845 -10.419  1.00  0.00
ATOM   1143  CD1 LEU   295      40.963  48.320  -9.266  1.00  0.00
ATOM   1144  CD2 LEU   295      39.785  47.625 -11.284  1.00  0.00
ATOM   1145  N   LYS   296      36.865  46.949 -10.693  1.00  0.00
ATOM   1146  CA  LYS   296      36.282  45.642 -10.337  1.00  0.00
ATOM   1147  C   LYS   296      34.766  45.733  -9.971  1.00  0.00
ATOM   1148  O   LYS   296      34.275  44.946  -9.165  1.00  0.00
ATOM   1149  CB  LYS   296      37.072  44.931  -9.236  1.00  0.00
ATOM   1150  CG  LYS   296      36.725  43.426  -9.149  1.00  0.00
ATOM   1151  CD  LYS   296      37.494  42.726  -8.045  1.00  0.00
ATOM   1152  CE  LYS   296      37.220  41.241  -7.954  1.00  0.00
ATOM   1153  NZ  LYS   296      37.575  40.714  -6.612  1.00  0.00
ATOM   1154  N   ASP   297      33.952  46.382 -10.816  1.00  0.00
ATOM   1155  CA  ASP   297      32.513  46.561 -10.681  1.00  0.00
ATOM   1156  C   ASP   297      32.095  47.164  -9.281  1.00  0.00
ATOM   1157  O   ASP   297      30.894  47.081  -8.956  1.00  0.00
ATOM   1158  CB  ASP   297      31.857  45.247 -10.961  1.00  0.00
ATOM   1159  CG  ASP   297      31.914  44.850 -12.387  1.00  0.00
ATOM   1160  OD1 ASP   297      32.020  45.703 -13.274  1.00  0.00
ATOM   1161  OD2 ASP   297      31.937  43.651 -12.635  1.00  0.00
ATOM   1162  N   HIS   298      32.984  47.852  -8.575  1.00  0.00
ATOM   1163  CA  HIS   298      32.654  48.395  -7.267  1.00  0.00
ATOM   1164  C   HIS   298      33.137  49.817  -7.099  1.00  0.00
ATOM   1165  O   HIS   298      34.331  50.035  -7.179  1.00  0.00
ATOM   1166  CB  HIS   298      33.360  47.502  -6.180  1.00  0.00
ATOM   1167  CG  HIS   298      32.798  46.105  -6.138  1.00  0.00
ATOM   1168  ND1 HIS   298      31.462  45.809  -6.353  1.00  0.00
ATOM   1169  CD2 HIS   298      33.423  44.915  -5.933  1.00  0.00
ATOM   1170  CE1 HIS   298      31.282  44.499  -6.280  1.00  0.00
ATOM   1171  NE2 HIS   298      32.456  43.934  -6.020  1.00  0.00
TER
END
