 
PFRMAT TS 
TARGET T0085 
AUTHOR 1204-1464-6170 
REMARK Minimized MODEL 
METHOD Sequence searches indicated that the N-terminal half of this  
METHOD protein bore homology to the four-heme structures 2CY3, 2CDU,  
METHOD 2CYM, etc.  The C-terminal half had homology to single-heme  
METHOD proteins like 1YEA.  2CYM and 1YEA were chosen as parent structures 
METHOD for the N- and C-terminal halves of the target, respectively. 
METHOD They were joined with a linker residue to form a two-domain  
METHOD scaffold.  Very crude insertions and deletions were made to  
METHOD create the starting scaffold.  Conserved residues were held in 
METHOD place, while non-conserved sidechains were built with SCWRL2.1 
METHOD (Bower et al, J. Mol. Biol., 1997, 267, 1268-1282)  
METHOD (see http://www.cmpharm.ucsf.edu/~bower/scwrl/scwrl.html).   
METHOD Sidechains in insertion and deletions were also free to move. 
METHOD Five heme molecules from the parent structures were used as  
METHOD steric clash checks.  Some local minimization of the backbone in the  
METHOD region of insertions and deletions was accomplished with the  
METHOD program Flo96, followed by another round of SCWRL. 
MODEL  1 REFINED 
PARENT N/A 
ATOM    694  N   GLY    93      -5.766   1.443 -32.157  1.00  0.00 
ATOM    695  CA  GLY    93      -4.455   1.629 -31.563  1.00  0.00 
ATOM    696  C   GLY    93      -3.732   2.789 -32.257  1.00  0.00 
ATOM    697  O   GLY    93      -3.675   2.821 -33.498  1.00  0.00 
ATOM    698  N   PRO    94      -3.234   3.653 -31.391  1.00  0.00 
ATOM    699  CA  PRO    94      -2.464   4.834 -31.850  1.00  0.00 
ATOM    700  C   PRO    94      -1.223   4.243 -32.484  1.00  0.00 
ATOM    701  O   PRO    94      -0.878   3.077 -32.189  1.00  0.00 
ATOM    702  CB  PRO    94      -2.191   5.596 -30.571  1.00  0.00 
ATOM    703  CG  PRO    94      -2.170   4.541 -29.500  1.00  0.00 
ATOM    704  CD  PRO    94      -3.279   3.570 -29.921  1.00  0.00 
ATOM    705  N   GLY    95      -0.691   4.917 -33.494  1.00  0.00 
ATOM    706  CA  GLY    95       0.540   4.318 -34.090  1.00  0.00 
ATOM    707  C   GLY    95       1.593   5.358 -33.691  1.00  0.00 
ATOM    708  O   GLY    95       1.163   6.523 -33.532  1.00  0.00 
ATOM    709  N   ARG    96       2.808   4.944 -33.500  1.00  0.00 
ATOM    710  CA  ARG    96       3.929   5.836 -33.139  1.00  0.00 
ATOM    711  C   ARG    96       4.362   6.548 -34.412  1.00  0.00 
ATOM    712  O   ARG    96       4.512   5.872 -35.452  1.00  0.00 
ATOM    713  CB  ARG    96       5.094   5.027 -32.565  1.00  0.00 
ATOM    714  CG  ARG    96       4.805   4.397 -31.212  1.00  0.00 
ATOM    715  CD  ARG    96       6.006   3.620 -30.697  1.00  0.00 
ATOM    716  NE  ARG    96       5.724   2.957 -29.426  1.00  0.00 
ATOM    717  CZ  ARG    96       6.557   2.116 -28.822  1.00  0.00 
ATOM    718  NH1 ARG    96       6.216   1.560 -27.667  1.00  0.00 
ATOM    719  NH2 ARG    96       7.729   1.832 -29.374  1.00  0.00 
ATOM    720  N   ASN    97       4.537   7.850 -34.352  1.00  0.00 
ATOM    721  CA  ASN    97       4.954   8.581 -35.568  1.00  0.00 
ATOM    722  C   ASN    97       6.290   8.060 -36.034  1.00  0.00 
ATOM    723  O   ASN    97       6.929   7.183 -35.427  1.00  0.00 
ATOM    724  CB  ASN    97       5.078  10.078 -35.277  1.00  0.00 
ATOM    725  CG  ASN    97       3.733  10.744 -35.067  1.00  0.00 
ATOM    726  OD1 ASN    97       2.956  10.906 -36.008  1.00  0.00 
ATOM    727  ND2 ASN    97       3.454  11.133 -33.828  1.00  0.00 
ATOM    728  N   PHE    98       6.722   8.551 -37.184  1.00  0.00 
ATOM    729  CA  PHE    98       8.046   8.113 -37.688  1.00  0.00 
ATOM    730  C   PHE    98       9.068   8.731 -36.720  1.00  0.00 
ATOM    731  O   PHE    98       8.744   9.172 -35.580  1.00  0.00 
ATOM    732  CB  PHE    98       8.267   8.612 -39.117  1.00  0.00 
ATOM    733  CG  PHE    98       7.343   7.992 -40.126  1.00  0.00 
ATOM    734  CD1 PHE    98       6.199   8.654 -40.537  1.00  0.00 
ATOM    735  CD2 PHE    98       7.618   6.747 -40.664  1.00  0.00 
ATOM    736  CE1 PHE    98       5.349   8.083 -41.465  1.00  0.00 
ATOM    737  CE2 PHE    98       6.768   6.176 -41.592  1.00  0.00 
ATOM    738  CZ  PHE    98       5.637   6.839 -41.993  1.00  0.00 
ATOM    739  N   ARG    99      10.303   8.687 -37.133  1.00  0.00 
ATOM    740  CA  ARG    99      11.364   9.313 -36.346  1.00  0.00 
ATOM    741  C   ARG    99      11.402  10.763 -36.859  1.00  0.00 
ATOM    742  O   ARG    99      10.607  11.123 -37.736  1.00  0.00 
ATOM    743  CB  ARG    99      12.696   8.596 -36.577  1.00  0.00 
ATOM    744  CG  ARG    99      12.700   7.139 -36.144  1.00  0.00 
ATOM    745  CD  ARG    99      14.054   6.494 -36.390  1.00  0.00 
ATOM    746  NE  ARG    99      14.057   5.076 -36.037  1.00  0.00 
ATOM    747  CZ  ARG    99      15.072   4.251 -36.269  1.00  0.00 
ATOM    748  NH1 ARG    99      14.985   2.976 -35.912  1.00  0.00 
ATOM    749  NH2 ARG    99      16.172   4.701 -36.857  1.00  0.00 
ATOM    750  N   GLY   100      12.340  11.465 -36.277  1.00  0.00 
ATOM    751  CA  GLY   100      12.599  12.838 -36.635  1.00  0.00 
ATOM    752  C   GLY   100      11.499  13.801 -36.281  1.00  0.00 
ATOM    753  O   GLY   100      11.226  14.691 -37.068  1.00  0.00 
ATOM    754  N   ASP   101      10.944  13.605 -35.075  1.00  0.00 
ATOM    755  CA  ASP   101       9.932  14.576 -34.630  1.00  0.00 
ATOM    756  C   ASP   101      10.730  15.733 -34.021  1.00  0.00 
ATOM    757  O   ASP   101      11.420  15.486 -33.038  1.00  0.00 
ATOM    758  CB  ASP   101       9.000  13.943 -33.595  1.00  0.00 
ATOM    759  CG  ASP   101       7.863  14.862 -33.194  1.00  0.00 
ATOM    760  OD1 ASP   101       7.088  14.488 -32.289  1.00  0.00 
ATOM    761  OD2 ASP   101       7.748  15.956 -33.786  1.00  0.00 
ATOM    762  N   HIS   102      10.568  16.947 -34.540  1.00  0.00 
ATOM    763  CA  HIS   102      11.310  18.087 -33.955  1.00  0.00 
ATOM    764  C   HIS   102      10.461  18.697 -32.858  1.00  0.00 
ATOM    765  O   HIS   102       9.229  18.912 -33.127  1.00  0.00 
ATOM    766  CB  HIS   102      11.600  19.143 -35.024  1.00  0.00 
ATOM    767  CG  HIS   102      12.505  18.664 -36.116  1.00  0.00 
ATOM    768  ND1 HIS   102      12.033  18.223 -37.334  1.00  0.00 
ATOM    769  CD2 HIS   102      13.943  18.510 -36.280  1.00  0.00 
ATOM    770  CE1 HIS   102      13.076  17.861 -38.102  1.00  0.00 
ATOM    771  NE2 HIS   102      14.225  18.030 -37.476  1.00  0.00 
ATOM    772  N   ARG   103      10.949  18.883 -31.672  1.00  0.00 
ATOM    773  CA  ARG   103      10.242  19.525 -30.523  1.00  0.00 
ATOM    774  C   ARG   103      10.845  20.940 -30.560  1.00  0.00 
ATOM    775  O   ARG   103      12.099  21.021 -30.439  1.00  0.00 
ATOM    776  CB  ARG   103      10.544  18.777 -29.223  1.00  0.00 
ATOM    777  CG  ARG   103       9.998  17.359 -29.182  1.00  0.00 
ATOM    778  CD  ARG   103      10.323  16.681 -27.861  1.00  0.00 
ATOM    779  NE  ARG   103       9.858  15.296 -27.828  1.00  0.00 
ATOM    780  CZ  ARG   103      10.122  14.443 -26.843  1.00  0.00 
ATOM    781  NH1 ARG   103       9.657  13.202 -26.899  1.00  0.00 
ATOM    782  NH2 ARG   103      10.849  14.832 -25.805  1.00  0.00 
ATOM    783  N   LYS   104      10.085  21.965 -30.852  1.00  0.00 
ATOM    784  CA  LYS   104      10.568  23.319 -31.005  1.00  0.00 
ATOM    785  C   LYS   104       9.767  24.440 -30.424  1.00  0.00 
ATOM    786  O   LYS   104       9.655  25.511 -31.081  1.00  0.00 
ATOM    787  CB  LYS   104      10.689  23.681 -32.487  1.00  0.00 
ATOM    788  CG  LYS   104      11.770  22.910 -33.227  1.00  0.00 
ATOM    789  CD  LYS   104      11.835  23.318 -34.690  1.00  0.00 
ATOM    790  CE  LYS   104      12.907  22.539 -35.434  1.00  0.00 
ATOM    791  NZ  LYS   104      12.958  22.902 -36.877  1.00  0.00 
ATOM    792  N   SER   105       9.196  24.207 -29.237  1.00  0.00 
ATOM    793  CA  SER   105       8.753  25.260 -28.340  1.00  0.00 
ATOM    794  C   SER   105       9.667  25.271 -27.110  1.00  0.00 
ATOM    795  O   SER   105       9.287  25.730 -26.031  1.00  0.00 
ATOM    796  CB  SER   105       7.309  25.015 -27.898  1.00  0.00 
ATOM    797  OG  SER   105       7.184  23.772 -27.229  1.00  0.00 
ATOM    798  N   GLY   106      10.881  24.726 -27.297  1.00  0.00 
ATOM    799  CA  GLY   106      11.827  24.365 -26.265  1.00  0.00 
ATOM    800  C   GLY   106      12.445  23.004 -26.612  1.00  0.00 
ATOM    801  O   GLY   106      12.374  22.575 -27.763  1.00  0.00 
TER 
END 
