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3D-Comp |
3D-Comp is intended for superposing tertiary structures of two proteins basing on alignment of their primary sequences.
Input data:
PDB file with the structure of protein 1;
PDB file with the structure of protein 2; and
Alignment of these protein sequences.
Output data:
PDB file with superposed structures;
RMSD of C-alpha atoms; and
Location parameters and rotation matrix.
Algorithm:
The method of best superposition of spatial structures independent
of their initial positions in the space (Kabsch, 1976) was realized.
Location parameters and rotation matrix are calculated according to C-alpha atoms.
Reference:
Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Cryst. 1976; A32: 922-923.
Program is provided with viewer.
Output example:
HEADER PROTEIN STRUCTURE ALIGNMENT COMPND (A) file1 chain 1 (B) file2 chain REMARK 1 REMARK 1 RMSD on Ca-atoms: 5.446 angstrom REMARK 1 REMARK 1 ATOM 1 N ARG A 4 -1.746 -1.551 -17.705 1.00 20.00 1TPH 159 ATOM 2 CA ARG A 4 -2.406 -0.969 -16.527 1.00 18.45 1TPH 160 ATOM 3 C ARG A 4 -3.056 0.346 -16.901 1.00 17.79 1TPH 161 ATOM 4 O ARG A 4 -2.402 1.285 -17.394 1.00 16.79 1TPH 162 ATOM 5 CB ARG A 4 -1.443 -0.773 -15.346 1.00 18.91 1TPH 163 ATOM 6 CG ARG A 4 -0.782 -2.095 -14.926 1.00 18.65 1TPH 164 ATOM 7 CD ARG A 4 0.107 -1.913 -13.747 1.00 17.90 1TPH 165 ATOM 8 NE ARG A 4 1.287 -1.143 -14.064 1.00 18.96 1TPH 166 ATOM 9 CZ ARG A 4 2.405 -1.563 -14.641 1.00 18.69 1TPH 167 ATOM 10 NH1 ARG A 4 2.536 -2.843 -14.958 1.00 18.24 1TPH 168 ATOM 11 NH2 ARG A 4 3.384 -0.688 -14.913 1.00 19.18 1TPH 169 ATOM 12 N LYS A 5 -4.354 0.388 -16.624 1.00 16.98 1TPH 170 ATOM 13 CA LYS A 5 -5.156 1.579 -16.897 1.00 17.05 1TPH 171 ATOM 14 C LYS A 5 -4.788 2.632 -15.872 1.00 16.14 1TPH 172 ATOM 15 O LYS A 5 -4.652 2.354 -14.659 1.00 15.95 1TPH 173 ATOM 16 CB LYS A 5 -6.642 1.226 -16.908 1.00 19.16 1TPH 174 ATOM 17 CG LYS A 5 -7.534 2.465 -17.082 1.00 20.61 1TPH 175 ATOM 18 CD LYS A 5 -8.928 2.025 -17.573 1.00 22.50 1TPH 176 ATOM 19 CE LYS A 5 -9.665 3.236 -18.130 1.00 23.76 1TPH 177 ATOM 20 NZ LYS A 5 -11.151 2.989 -18.150 1.00 26.08 1TPH 178 ATOM 21 N PHE A 6 -4.557 3.846 -16.358 1.00 15.28 1TPH 179 ATOM 22 CA PHE A 6 -4.179 5.021 -15.595 1.00 14.42 1TPH 180 ATOM 23 C PHE A 6 -5.357 5.270 -14.614 1.00 13.74 1TPH 181 ATOM 24 O PHE A 6 -6.506 5.243 -15.104 1.00 13.74 1TPH 182 ATOM 25 CB PHE A 6 -3.896 6.242 -16.480 1.00 15.45 1TPH 183 ATOM 26 CG PHE A 6 -3.145 7.348 -15.810 1.00 16.58 1TPH 184 ATOM 27 CD1 PHE A 6 -1.848 7.118 -15.336 1.00 17.22 1TPH 185 ATOM 28 CD2 PHE A 6 -3.706 8.602 -15.691 1.00 17.37 1TPH 186 ATOM 29 CE1 PHE A 6 -1.140 8.146 -14.694 1.00 18.11 1TPH 187 ATOM 30 CE2 PHE A 6 -3.017 9.650 -15.076 1.00 18.16 1TPH 188 ... ATOM 1851 CG HIS A 248 -4.280 13.013 -22.863 1.00 37.01 1TPH2009 ATOM 1852 ND1 HIS A 248 -3.586 11.841 -22.990 1.00 37.77 1TPH2010 ATOM 1853 CD2 HIS A 248 -5.615 12.740 -22.796 1.00 37.69 1TPH2011 ATOM 1854 CE1 HIS A 248 -4.480 10.881 -22.987 1.00 38.21 1TPH2012 ATOM 1855 NE2 HIS A 248 -5.735 11.367 -22.869 1.00 38.19 1TPH2013 ATOM 1856 OXT HIS A 248 -0.450 15.834 -22.118 1.00 35.78 1TPH2014 ATOM 7 N THR B 1 -12.933 -5.682 -10.516 1.00 40.52 1LAP 103 ATOM 8 CA THR B 1 -13.050 -4.941 -9.274 1.00 39.43 1LAP 104 ATOM 9 C THR B 1 -11.679 -4.319 -8.996 1.00 37.36 1LAP 105 ATOM 10 O THR B 1 -10.702 -4.657 -9.687 1.00 38.20 1LAP 106 ATOM 11 CB THR B 1 -13.495 -5.968 -8.212 1.00 38.53 1LAP 107 ATOM 12 OG1 THR B 1 -12.792 -7.189 -8.461 1.00 37.44 1LAP 108 ATOM 13 CG2 THR B 1 -14.999 -6.211 -8.275 1.00 39.48 1LAP 109 ATOM 14 1H THR B 1 -12.541 -5.056 -11.248 1.00 20.00 1LAP 110 ATOM 15 2H THR B 1 -12.192 -6.364 -10.254 1.00 20.00 1LAP 111 ATOM 16 3H THR B 1 -13.808 -6.180 -10.765 1.00 20.00 1LAP 112 ATOM 17 HG1 THR B 1 -12.958 -7.792 -7.718 1.00 20.00 1LAP 113 ATOM 21 N LYS B 2 -11.652 -3.361 -8.089 1.00 30.72 1LAP 114 ATOM 22 CA LYS B 2 -10.408 -2.765 -7.685 1.00 30.00 1LAP 115 ATOM 23 C LYS B 2 -10.248 -3.003 -6.195 1.00 28.26 1LAP 116 ATOM 24 O LYS B 2 -11.216 -3.239 -5.461 1.00 29.56 1LAP 117 ATOM 25 CB LYS B 2 -10.396 -1.271 -7.916 1.00 29.35 1LAP 118 ATOM 26 CG LYS B 2 -10.170 -0.836 -9.334 1.00 29.97 1LAP 119 ATOM 27 CD LYS B 2 -10.243 0.686 -9.378 1.00 32.46 1LAP 120 ATOM 28 CE LYS B 2 -11.669 1.234 -9.258 1.00 34.49 1LAP 121 ATOM 29 NZ LYS B 2 -11.710 2.684 -9.110 1.00 34.65 1LAP 122 ATOM 30 H LYS B 2 -12.450 -3.023 -7.621 1.00 20.00 1LAP 123 ... ATOM 7451 C GLN B 484 24.036 16.260 -12.472 1.00 47.41 1LAP4582 ATOM 7452 O GLN B 484 24.945 15.910 -13.247 1.00 51.49 1LAP4583 ATOM 7453 CB GLN B 484 22.078 15.664 -11.064 1.00 42.25 1LAP4584 ATOM 7454 CG GLN B 484 21.119 14.544 -10.749 1.00 44.93 1LAP4585 ATOM 7455 CD GLN B 484 19.652 14.871 -10.669 1.00 45.32 1LAP4586 ATOM 7456 OE1 GLN B 484 18.988 15.253 -11.631 1.00 45.98 1LAP4587 ATOM 7457 NE2 GLN B 484 19.131 14.720 -9.457 1.00 43.27 1LAP4588 ATOM 7458 H GLN B 484 23.100 13.479 -12.156 1.00 20.00 1LAP4589 ATOM 7459 1HE2 GLN B 484 18.183 14.944 -9.379 1.00 20.00 1LAP4590 ATOM 7460 2HE2 GLN B 484 19.711 14.419 -8.732 1.00 20.00 1LAP4591 TER END