
#######################################################
#                                                     #
#                        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    6 (   56),  selected    6 , name T0320TS277_3-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS277_3-D2.T0320_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    -       -      N     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    -       -      N     233           -
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    -       -      N     242           -
LGA    -       -      P     243           -
LGA    -       -      A     244           -
LGA    -       -      L     245           -
LGA    -       -      H     246           -
LGA    -       -      F     247           -
LGA    -       -      E     248           -
LGA    -       -      W     249           -
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    -       -      A     254           -
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    -       -      S     264           -
LGA    -       -      S     265           -
LGA    -       -      A     266           -
LGA    -       -      I     267           -
LGA    -       -      N     268           -
LGA    -       -      T     269           -
LGA    N     228      S     270          1.166
LGA    N     229      P     271          2.820
LGA    S     230      I     272          1.144
LGA    L     231      S     273          2.618
LGA    P     232      V     274          1.472
LGA    N     233      V     275          1.804
LGA    -       -      D     276           -
LGA    -       -      K     277           -
LGA    -       -      E     278           -
LGA    -       -      R     279           -
LGA    -       -      F     280           -
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    -       -      Y     283           -
LGA    -       -      H     284           -
LGA    -       -      D     285           -
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      E     299           -
LGA    -       -      R     300           -
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    -       -      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    6   73    5.0      6    1.95     0.00      7.612     0.292

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.531052 * X  +  -0.211974 * Y  +  -0.820397 * Z  +  66.635696
  Y_new =  -0.764118 * X  +  -0.538244 * Y  +  -0.355551 * Z  +  45.794102
  Z_new =  -0.366206 * X  +   0.815696 * Y  +  -0.447809 * Z  +  11.686414 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.072864   -1.068729  [ DEG:   118.7663    -61.2337 ]
  Theta =   0.374928    2.766664  [ DEG:    21.4818    158.5182 ]
  Phi   =  -0.963443    2.178150  [ DEG:   -55.2012    124.7988 ]
 
# 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: T0320TS277_3-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS277_3-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6   73   5.0    6   1.95    0.00   7.612
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS277_3-D2
PFRMAT TS 
TARGET T0320
MODEL 3
PARENT 1WY5_A
ATOM   4063  H   ASN   228      10.711  30.672   5.957  1.00  0.00                              
ATOM   4065  N   ASN   228      10.498  31.523   6.293  1.00  0.00                              
ATOM   4067  CA  ASN   228      11.519  32.281   7.048  1.00  0.00                              
ATOM   4069  CB  ASN   228      11.009  32.616   8.438  1.00  0.00                              
ATOM   4071  C   ASN   228      12.849  31.540   7.152  1.00  0.00                              
ATOM   4073  O   ASN   228      13.156  30.955   8.202  1.00  0.00                              
ATOM   4075  CG  ASN   228      11.984  33.467   9.212  1.00  0.00                              
ATOM   4077  ND2 ASN   228      11.825  33.512  10.533  1.00  0.00                              
ATOM   4079 HD21 ASN   228      11.110  33.029  10.919  1.00  0.00                              
ATOM   4081 HD22 ASN   228      12.431  34.011  11.057  1.00  0.00                              
ATOM   4083  OD1 ASN   228      12.891  34.060   8.639  1.00  0.00                              
ATOM   4085  H   ASN   229      13.404  32.049   5.311  1.00  0.00                              
ATOM   4087  N   ASN   229      13.676  31.597   6.092  1.00  0.00                              
ATOM   4089  CA  ASN   229      15.018  30.926   6.123  1.00  0.00                              
ATOM   4091  CB  ASN   229      14.899  29.426   6.510  1.00  0.00                              
ATOM   4093  C   ASN   229      15.782  31.083   4.804  1.00  0.00                              
ATOM   4095  O   ASN   229      15.419  30.470   3.787  1.00  0.00                              
ATOM   4097  CG  ASN   229      16.267  28.783   6.809  1.00  0.00                              
ATOM   4099  ND2 ASN   229      16.459  27.533   6.356  1.00  0.00                              
ATOM   4101 HD21 ASN   229      15.762  27.112   5.883  1.00  0.00                              
ATOM   4103 HD22 ASN   229      17.279  27.098   6.530  1.00  0.00                              
ATOM   4105  OD1 ASN   229      17.115  29.384   7.471  1.00  0.00                              
ATOM   4107  H   SER   230      17.028  32.335   5.617  1.00  0.00                              
ATOM   4109  N   SER   230      16.791  31.912   4.819  1.00  0.00                              
ATOM   4111  CA  SER   230      17.620  32.167   3.614  1.00  0.00                              
ATOM   4113  CB  SER   230      17.123  31.332   2.407  1.00  0.00                              
ATOM   4115  C   SER   230      17.722  33.705   3.218  1.00  0.00                              
ATOM   4117  O   SER   230      17.238  34.592   3.929  1.00  0.00                              
ATOM   4119  OG  SER   230      15.904  31.860   1.882  1.00  0.00                              
ATOM   4121  H   LEU   231      18.523  33.202   1.514  1.00  0.00                              
ATOM   4123  N   LEU   231      18.303  33.941   2.055  1.00  0.00                              
ATOM   4125  CA  LEU   231      18.578  35.297   1.525  1.00  0.00                              
ATOM   4127  CB  LEU   231      18.834  36.325   2.631  1.00  0.00                              
ATOM   4129  C   LEU   231      19.785  35.216   0.657  1.00  0.00                              
ATOM   4131  O   LEU   231      19.730  35.539  -0.507  1.00  0.00                              
ATOM   4133  CG  LEU   231      19.251  37.721   2.143  1.00  0.00                              
ATOM   4135  CD1 LEU   231      18.036  38.499   1.662  1.00  0.00                              
ATOM   4137  CD2 LEU   231      19.968  38.469   3.231  1.00  0.00                              
ATOM   4139  N   PRO   232      20.918  34.818   1.237  1.00  0.00                              
ATOM   4141  CA  PRO   232      22.136  34.697   0.501  1.00  0.00                              
ATOM   4143  CB  PRO   232      23.182  35.044   1.527  1.00  0.00                              
ATOM   4145  C   PRO   232      22.323  33.275  -0.018  1.00  0.00                              
ATOM   4147  O   PRO   232      21.714  32.890  -1.026  1.00  0.00                              
ATOM   4149  CG  PRO   232      22.653  34.420   2.787  1.00  0.00                              
ATOM   4151  CD  PRO   232      21.124  34.511   2.662  1.00  0.00                              
ATOM   4153  H   ASN   233      23.567  32.824   1.449  1.00  0.00                              
ATOM   4155  N   ASN   233      23.133  32.480   0.690  1.00  0.00                              
ATOM   4157  CA  ASN   233      23.353  31.079   0.324  1.00  0.00                              
ATOM   4159  CB  ASN   233      24.106  30.346   1.449  1.00  0.00                              
ATOM   4161  C   ASN   233      22.035  30.372   0.030  1.00  0.00                              
ATOM   4163  O   ASN   233      22.023  29.293  -0.566  1.00  0.00                              
ATOM   4165  CG  ASN   233      24.593  28.966   1.031  1.00  0.00                              
ATOM   4167  ND2 ASN   233      24.048  27.931   1.653  1.00  0.00                              
ATOM   4169 HD21 ASN   233      23.388  28.093   2.304  1.00  0.00                              
ATOM   4171 HD22 ASN   233      24.326  27.058   1.431  1.00  0.00                              
ATOM   4173  OD1 ASN   233      25.433  28.834   0.136  1.00  0.00                              
TER 
END
