
#######################################################
#                                                     #
#                        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 (   86),  selected    9 , name T0372TS277_4-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS277_4-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          2.474
LGA    Y     291      R      78          0.944
LGA    M     292      K      79          1.398
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    A     293      E      82          1.734
LGA    C     294      D      83          1.693
LGA    -       -      A      84           -
LGA    -       -      D      85           -
LGA    L     295      K      86          0.798
LGA    -       -      E      87           -
LGA    K     296      K      88          1.834
LGA    D     297      H      89          0.608
LGA    H     298      N      90          1.802
LGA    -       -      F      91           -
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    1.58    11.11      6.656     0.536

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.448840 * X  +  -0.705838 * Y  +  -0.548029 * Z  +  46.611107
  Y_new =   0.401763 * X  +   0.388403 * Y  +  -0.829294 * Z  +  59.250141
  Z_new =   0.798203 * X  +  -0.592399 * Y  +   0.109249 * Z  +  -0.680541 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.388427    1.753165  [ DEG:   -79.5510    100.4490 ]
  Theta =  -0.924307   -2.217286  [ DEG:   -52.9589   -127.0411 ]
  Phi   =   2.411483   -0.730110  [ DEG:   138.1678    -41.8322 ]
 
# 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: T0372TS277_4-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS277_4-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   1.58   11.11   6.656
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS277_4-D1
PFRMAT TS 
TARGET T0372
MODEL 4
PARENT 1KUV_A
ATOM   2963  H   LYS   290      29.112  57.088  -6.789  1.00  0.00                              
ATOM   2965  N   LYS   290      29.716  57.308  -7.488  1.00  0.00                              
ATOM   2967  CA  LYS   290      30.882  58.146  -7.182  1.00  0.00                              
ATOM   2969  CB  LYS   290      31.100  58.245  -5.666  1.00  0.00                              
ATOM   2971  C   LYS   290      32.113  57.550  -7.857  1.00  0.00                              
ATOM   2973  O   LYS   290      32.277  56.327  -7.882  1.00  0.00                              
ATOM   2975  CG  LYS   290      31.892  59.458  -5.188  1.00  0.00                              
ATOM   2977  CD  LYS   290      31.732  59.675  -3.688  1.00  0.00                              
ATOM   2979  CE  LYS   290      30.854  60.882  -3.385  1.00  0.00                              
ATOM   2981  NZ  LYS   290      30.260  60.807  -2.018  1.00  0.00                              
ATOM   2983  H   TYR   291      32.940  59.315  -8.244  1.00  0.00                              
ATOM   2985  N   TYR   291      33.015  58.383  -8.378  1.00  0.00                              
ATOM   2987  CA  TYR   291      34.139  57.846  -9.144  1.00  0.00                              
ATOM   2989  CB  TYR   291      34.127  58.371 -10.573  1.00  0.00                              
ATOM   2991  C   TYR   291      35.522  58.059  -8.542  1.00  0.00                              
ATOM   2993  O   TYR   291      35.885  59.164  -8.131  1.00  0.00                              
ATOM   2995  CG  TYR   291      33.998  59.868 -10.655  1.00  0.00                              
ATOM   2997  CD1 TYR   291      35.118  60.690 -10.715  1.00  0.00                              
ATOM   2999  CE1 TYR   291      34.990  62.070 -10.821  1.00  0.00                              
ATOM   3001  CZ  TYR   291      33.728  62.631 -10.896  1.00  0.00                              
ATOM   3003  CD2 TYR   291      32.742  60.465 -10.629  1.00  0.00                              
ATOM   3005  CE2 TYR   291      32.601  61.838 -10.765  1.00  0.00                              
ATOM   3007  OH  TYR   291      33.591  64.002 -10.955  1.00  0.00                              
ATOM   3009  H   MET   292      35.931  56.170  -8.876  1.00  0.00                              
ATOM   3011  N   MET   292      36.304  56.978  -8.556  1.00  0.00                              
ATOM   3013  CA  MET   292      37.697  56.969  -8.114  1.00  0.00                              
ATOM   3015  CB  MET   292      37.768  56.449  -6.674  1.00  0.00                              
ATOM   3017  C   MET   292      38.483  56.035  -9.043  1.00  0.00                              
ATOM   3019  O   MET   292      39.269  55.199  -8.593  1.00  0.00                              
ATOM   3021  CG  MET   292      39.101  56.677  -5.976  1.00  0.00                              
ATOM   3023  SD  MET   292      39.269  55.675  -4.480  1.00  0.00                              
ATOM   3025  CE  MET   292      38.962  56.904  -3.222  1.00  0.00                              
ATOM   3027  H   ALA   293      37.627  56.855 -10.588  1.00  0.00                              
ATOM   3029  N   ALA   293      38.224  56.181 -10.342  1.00  0.00                              
ATOM   3031  CA  ALA   293      38.770  55.350 -11.423  1.00  0.00                              
ATOM   3033  CB  ALA   293      39.072  56.234 -12.630  1.00  0.00                              
ATOM   3035  C   ALA   293      40.003  54.499 -11.096  1.00  0.00                              
ATOM   3037  O   ALA   293      41.078  55.022 -10.794  1.00  0.00                              
ATOM   3039  H   CYS   294      39.006  52.842 -11.423  1.00  0.00                              
ATOM   3041  N   CYS   294      39.854  53.178 -11.232  1.00  0.00                              
ATOM   3043  CA  CYS   294      40.961  52.231 -11.073  1.00  0.00                              
ATOM   3045  CB  CYS   294      40.787  51.337  -9.841  1.00  0.00                              
ATOM   3047  C   CYS   294      41.139  51.381 -12.336  1.00  0.00                              
ATOM   3049  O   CYS   294      41.943  51.749 -13.198  1.00  0.00                              
ATOM   3051  SG  CYS   294      40.346  52.226  -8.326  1.00  0.00                              
ATOM   3053  H   LEU   295      39.907  49.930 -11.758  1.00  0.00                              
ATOM   3055  N   LEU   295      40.459  50.237 -12.464  1.00  0.00                              
ATOM   3057  CA  LEU   295      40.551  49.469 -13.711  1.00  0.00                              
ATOM   3059  CB  LEU   295      42.010  49.302 -14.154  1.00  0.00                              
ATOM   3061  C   LEU   295      39.871  48.097 -13.710  1.00  0.00                              
ATOM   3063  O   LEU   295      40.516  47.093 -13.400  1.00  0.00                              
ATOM   3065  CG  LEU   295      42.231  48.577 -15.485  1.00  0.00                              
ATOM   3067  CD1 LEU   295      41.556  49.342 -16.616  1.00  0.00                              
ATOM   3069  CD2 LEU   295      43.718  48.419 -15.762  1.00  0.00                              
ATOM   3071  H   LYS   296      38.156  48.866 -14.295  1.00  0.00                              
ATOM   3073  N   LYS   296      38.601  48.047 -14.118  1.00  0.00                              
ATOM   3075  CA  LYS   296      37.867  46.789 -14.294  1.00  0.00                              
ATOM   3077  CB  LYS   296      38.644  45.859 -15.227  1.00  0.00                              
ATOM   3079  C   LYS   296      37.479  46.038 -13.014  1.00  0.00                              
ATOM   3081  O   LYS   296      38.284  45.896 -12.093  1.00  0.00                              
ATOM   3083  CG  LYS   296      38.960  46.460 -16.591  1.00  0.00                              
ATOM   3085  CD  LYS   296      39.759  45.492 -17.456  1.00  0.00                              
ATOM   3087  CE  LYS   296      39.839  45.955 -18.906  1.00  0.00                              
ATOM   3089  NZ  LYS   296      40.571  44.975 -19.762  1.00  0.00                              
ATOM   3091  H   ASP   297      35.675  45.679 -13.719  1.00  0.00                              
ATOM   3093  N   ASP   297      36.250  45.510 -12.991  1.00  0.00                              
ATOM   3095  CA  ASP   297      35.740  44.685 -11.888  1.00  0.00                              
ATOM   3097  CB  ASP   297      36.820  44.330 -10.861  1.00  0.00                              
ATOM   3099  C   ASP   297      34.564  45.328 -11.164  1.00  0.00                              
ATOM   3101  O   ASP   297      33.901  46.218 -11.700  1.00  0.00                              
ATOM   3103  CG  ASP   297      37.608  43.098 -11.254  1.00  0.00                              
ATOM   3105  OD1 ASP   297      37.286  42.492 -12.297  1.00  0.00                              
ATOM   3107  OD2 ASP   297      38.544  42.716 -10.519  1.00  0.00                              
ATOM   3109  H   HIS   298      34.751  44.074  -9.651  1.00  0.00                              
ATOM   3111  N   HIS   298      34.279  44.832  -9.963  1.00  0.00                              
ATOM   3113  CA  HIS   298      33.249  45.428  -9.121  1.00  0.00                              
ATOM   3115  CB  HIS   298      32.945  44.497  -7.943  1.00  0.00                              
ATOM   3117  C   HIS   298      33.748  46.773  -8.602  1.00  0.00                              
ATOM   3119  O   HIS   298      34.951  46.928  -8.388  1.00  0.00                              
ATOM   3121  CG  HIS   298      32.386  43.174  -8.368  1.00  0.00                              
ATOM   3123  ND1 HIS   298      31.058  42.997  -8.691  1.00  0.00                              
ATOM   3125  HD1 HIS   298      30.380  43.664  -8.651  1.00  0.00                              
ATOM   3127  CE1 HIS   298      30.847  41.724  -8.980  1.00  0.00                              
ATOM   3129  NE2 HIS   298      31.990  41.071  -8.854  1.00  0.00                              
ATOM   3131  HE2 HIS   298      32.094  40.133  -8.964  1.00  0.00                              
ATOM   3133  CD2 HIS   298      32.962  41.948  -8.440  1.00  0.00                              
TER 
END
