
#######################################################
#                                                     #
#                        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   44 (   44),  selected   44 , name T0356TS464_2-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356TS464_2-D3.T0356_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    E     359      F     348           -
LGA    G     360      P     349           -
LGA    -       -      E     350           -
LGA    -       -      I     351           -
LGA    -       -      V     352           -
LGA    -       -      D     353           -
LGA    -       -      F     354           -
LGA    -       -      Y     355           -
LGA    -       -      L     356           -
LGA    -       -      P     357           -
LGA    -       -      P     358           -
LGA    -       -      E     359           -
LGA    -       -      G     360           -
LGA    -       -      C     361           -
LGA    -       -      S     362           -
LGA    -       -      Y     363           -
LGA    -       -      R     364           -
LGA    -       -      L     365           -
LGA    -       -      A     366           -
LGA    -       -      V     367           -
LGA    -       -      V     368           -
LGA    -       -      T     369           -
LGA    -       -      I     370           -
LGA    -       -      K     371           -
LGA    C     361      K     372          3.258
LGA    -       -      Q     373           -
LGA    S     362      Y     374          2.181
LGA    Y     363      A     375          1.560
LGA    R     364      G     376          1.602
LGA    L     365      H     377          1.158
LGA    A     366      A     378          1.105
LGA    V     367      K     379          0.751
LGA    V     368      R     380          0.648
LGA    T     369      V     381          0.578
LGA    I     370      M     382          1.195
LGA    K     371      M     383          1.316
LGA    K     372      G     384          1.757
LGA    Q     373      V     385          1.858
LGA    Y     374      W     386          1.686
LGA    A     375      S     387          1.799
LGA    G     376      F     388          1.730
LGA    H     377      L     389          3.139
LGA    -       -      R     390           -
LGA    -       -      Q     391           -
LGA    A     378      F     392          1.476
LGA    K     379      M     393          1.904
LGA    -       -      Y     394           -
LGA    R     380      T     395          2.348
LGA    V     381      K     396          3.417
LGA    M     382      F     397          1.906
LGA    M     383      V     398          3.193
LGA    G     384      I     399          2.823
LGA    K     396      -       -           -
LGA    F     397      -       -           -
LGA    V     398      -       -           -
LGA    I     399      -       -           -
LGA    V     400      -       -           -
LGA    C     401      V     400          0.939
LGA    D     402      C     401          1.546
LGA    I     435      D     402           -
LGA    D     436      D     403           -
LGA    Y     437      D     404           -
LGA    L     438      V     405           -
LGA    D     439      N     406           -
LGA    S     445      A     407           -
LGA    -       -      R     408           -
LGA    -       -      D     409           -
LGA    -       -      W     410           -
LGA    -       -      N     411           -
LGA    -       -      D     412           -
LGA    -       -      V     413           -
LGA    -       -      I     414           -
LGA    -       -      W     415           -
LGA    -       -      A     416           -
LGA    -       -      I     417           -
LGA    -       -      T     418           -
LGA    -       -      T     419           -
LGA    -       -      R     420           -
LGA    -       -      M     421           -
LGA    -       -      D     422           -
LGA    -       -      P     423           -
LGA    -       -      A     424           -
LGA    -       -      R     425           -
LGA    G     446      D     426          3.265
LGA    -       -      T     427           -
LGA    -       -      V     428           -
LGA    -       -      L     429           -
LGA    -       -      V     430           -
LGA    -       -      E     431           -
LGA    -       -      N     432           -
LGA    -       -      T     433           -
LGA    -       -      P     434           -
LGA    -       -      I     435           -
LGA    -       -      D     436           -
LGA    -       -      Y     437           -
LGA    -       -      L     438           -
LGA    -       -      D     439           -
LGA    -       -      F     440           -
LGA    -       -      A     441           -
LGA    -       -      S     442           -
LGA    -       -      P     443           -
LGA    -       -      V     444           -
LGA    -       -      S     445           -
LGA    -       -      G     446           -
LGA    -       -      L     447           -
LGA    -       -      G     448           -
LGA    -       -      S     449           -
LGA    -       -      K     450           -
LGA    -       -      M     451           -
LGA    -       -      G     452           -
LGA    -       -      L     453           -
LGA    -       -      D     454           -
LGA    L     447      A     455          2.327
LGA    G     448      T     456          3.381
LGA    S     449      N     457          3.145
LGA    K     450      K     458          5.048
LGA    -       -      W     459           -
LGA    -       -      P     460           -
LGA    -       -      G     461           -
LGA    -       -      E     462           -
LGA    -       -      T     463           -
LGA    -       -      Q     464           -
LGA    -       -      R     465           -
LGA    -       -      E     466           -
LGA    -       -      W     467           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44  120    5.0     31    2.30     6.45     21.155     1.292

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.622281 * X  +   0.782768 * Y  +   0.006368 * Z  +  37.125065
  Y_new =  -0.358642 * X  +  -0.277861 * Y  +  -0.891162 * Z  +  54.856682
  Z_new =  -0.695804 * X  +  -0.556837 * Y  +   0.453641 * Z  +  76.847145 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.887171    2.254421  [ DEG:   -50.8312    129.1688 ]
  Theta =   0.769538    2.372054  [ DEG:    44.0913    135.9087 ]
  Phi   =  -2.618756    0.522836  [ DEG:  -150.0437     29.9563 ]
 
# 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: T0356TS464_2-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS464_2-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44  120   5.0   31   2.30    6.45  21.155
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS464_2-D3
PFRMAT TS
TARGET T0356
MODEL 2
PARENT N/A
ATOM    107  CA  GLU   359      40.270  68.620  53.401  1.00  0.00
ATOM    108  CA  GLY   360      40.139  68.872  49.613  1.00  0.00
ATOM    109  CA  CYS   361      43.775  68.120  48.873  1.00  0.00
ATOM    110  CA  SER   362      44.874  66.577  45.562  1.00  0.00
ATOM    111  CA  TYR   363      44.753  62.769  45.650  1.00  0.00
ATOM    112  CA  ARG   364      47.941  61.536  47.279  1.00  0.00
ATOM    113  CA  LEU   365      48.860  64.638  49.273  1.00  0.00
ATOM    114  CA  ALA   366      48.386  63.299  52.800  1.00  0.00
ATOM    115  CA  VAL   367      50.243  60.146  51.768  1.00  0.00
ATOM    116  CA  VAL   368      53.208  62.184  50.518  1.00  0.00
ATOM    117  CA  THR   369      53.425  64.002  53.876  1.00  0.00
ATOM    118  CA  ILE   370      53.517  60.633  55.657  1.00  0.00
ATOM    119  CA  LYS   371      56.430  59.124  53.478  1.00  0.00
ATOM    120  CA  LYS   372      58.770  62.178  53.589  1.00  0.00
ATOM    121  CA  GLN   373      58.453  62.224  57.487  1.00  0.00
ATOM    122  CA  TYR   374      59.144  58.410  57.677  1.00  0.00
ATOM    123  CA  ALA   375      62.258  58.814  55.382  1.00  0.00
ATOM    124  CA  GLY   376      63.468  61.670  57.735  1.00  0.00
ATOM    125  CA  HIS   377      63.237  59.569  60.953  1.00  0.00
ATOM    126  CA  ALA   378      59.626  59.418  62.181  1.00  0.00
ATOM    127  CA  LYS   379      59.027  55.867  63.476  1.00  0.00
ATOM    128  CA  ARG   380      55.245  55.344  63.858  1.00  0.00
ATOM    129  CA  VAL   381      52.326  57.114  62.066  1.00  0.00
ATOM    130  CA  MET   382      49.480  59.061  63.750  1.00  0.00
ATOM    131  CA  MET   383      46.508  60.139  61.650  1.00  0.00
ATOM    132  CA  GLY   384      44.557  63.356  62.108  1.00  0.00
ATOM    133  CA  LYS   396      58.751  59.051  67.545  1.00  0.00
ATOM    134  CA  PHE   397      55.076  59.367  66.537  1.00  0.00
ATOM    135  CA  VAL   398      54.068  62.678  65.002  1.00  0.00
ATOM    136  CA  ILE   399      50.343  63.275  64.546  1.00  0.00
ATOM    137  CA  VAL   400      49.559  64.680  61.069  1.00  0.00
ATOM    138  CA  CYS   401      46.993  64.956  58.311  1.00  0.00
ATOM    139  CA  ASP   402      45.482  67.731  56.165  1.00  0.00
ATOM    140  CA  ILE   435      55.299  48.836  51.089  1.00  0.00
ATOM    141  CA  ASP   436      54.410  52.620  50.640  1.00  0.00
ATOM    142  CA  TYR   437      52.597  52.355  47.256  1.00  0.00
ATOM    143  CA  LEU   438      50.987  50.120  44.821  1.00  0.00
ATOM    144  CA  ASP   439      51.456  50.133  41.031  1.00  0.00
ATOM    145  CA  SER   445      42.475  59.032  50.687  1.00  0.00
ATOM    146  CA  GLY   446      39.738  59.877  53.171  1.00  0.00
ATOM    147  CA  LEU   447      41.825  62.746  54.580  1.00  0.00
ATOM    148  CA  GLY   448      42.644  64.032  51.087  1.00  0.00
ATOM    149  CA  SER   449      38.919  64.232  50.386  1.00  0.00
ATOM    150  CA  LYS   450      37.909  65.666  53.752  1.00  0.00
TER
END
