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.
Output example:
HEADER PROTEIN STRUCTURE ALIGNMENT
COMPND (A) file1 chain A (B) file2 chain B
REMARK 1
REMARK 1 Transformation of chain A coordinates:
REMARK 1 Anew = U*(Aold-shift1)+shift2
REMARK 1 The rotation matrix U:
REMARK 1 0.2843 0.9037 0.3184
REMARK 1 -0.3886 -0.1940 0.9003
REMARK 1 0.8767 -0.3809 0.2969
REMARK 1
REMARK 1 shift1 (X, Y, Z) = ( 24.434, 9.342, 8.358)
REMARK 1 shift2 (X, Y, Z) = ( 25.967, 64.677, 13.625)
REMARK 1
REMARK 1 RMSD on Ca-atoms: 3.684 angstrom
REMARK 1
ATOM 1 N MET A 1 38.730 55.215 -3.247 1.00 0.00
ATOM 2 CA MET A 1 38.092 55.938 -2.140 1.00 0.00
ATOM 3 C MET A 1 36.924 56.821 -2.592 1.00 0.00
ATOM 4 O MET A 1 37.119 57.872 -3.206 1.00 0.00
ATOM 5 CB MET A 1 39.133 56.786 -1.392 1.00 0.00
ATOM 6 CG MET A 1 38.587 57.621 -0.216 1.00 0.00
ATOM 7 SD MET A 1 37.784 56.643 1.092 1.00 0.00
ATOM 8 CE MET A 1 39.147 56.452 2.275 1.00 0.00
ATOM 9 N GLN A 2 35.708 56.384 -2.279 1.00 0.00
ATOM 10 CA GLN A 2 34.509 57.134 -2.635 1.00 0.00
ATOM 11 C GLN A 2 33.808 57.700 -1.397 1.00 0.00
ATOM 12 O GLN A 2 34.004 57.211 -0.285 1.00 0.00
ATOM 13 CB GLN A 2 33.546 56.247 -3.414 1.00 0.00
ATOM 14 CG GLN A 2 34.062 55.820 -4.780 1.00 0.00
ATOM 15 CD GLN A 2 33.012 55.077 -5.594 1.00 0.00
ATOM 16 OE1 GLN A 2 31.804 55.288 -5.421 1.00 0.00
ATOM 17 NE2 GLN A 2 33.468 54.204 -6.493 1.00 0.00
ATOM 18 N THR A 3 32.998 58.738 -1.593 1.00 0.00
ATOM 19 CA THR A 3 32.277 59.357 -0.488 1.00 0.00
ATOM 20 C THR A 3 30.778 59.069 -0.511 1.00 0.00
ATOM 21 O THR A 3 30.168 58.918 -1.578 1.00 0.00
ATOM 22 CB THR A 3 32.488 60.881 -0.457 1.00 0.00
ATOM 23 OG1 THR A 3 33.891 61.165 -0.440 1.00 0.00
ATOM 24 CG2 THR A 3 31.844 61.495 0.797 1.00 0.00
ATOM 25 N ILE A 4 30.215 58.923 0.686 1.00 0.00
ATOM 26 CA ILE A 4 28.785 58.693 0.871 1.00 0.00
ATOM 27 C ILE A 4 28.292 59.883 1.697 1.00 0.00
ATOM 28 O ILE A 4 28.614 59.996 2.881 1.00 0.00
ATOM 29 CB ILE A 4 28.490 57.386 1.652 1.00 0.00
……………………..
ATOM 2962 CB LEU B 385 7.514 70.764 -17.815 1.00 0.00
ATOM 2963 CG LEU B 385 7.267 70.676 -16.308 1.00 0.00
ATOM 2964 CD1 LEU B 385 6.707 71.973 -15.753 1.00 0.00
ATOM 2965 CD2 LEU B 385 6.317 69.529 -15.982 1.00 0.00
ATOM 2966 N SER B 386 9.587 69.697 -20.509 1.00 0.00
ATOM 2967 CA SER B 386 9.716 69.739 -21.951 1.00 0.00
ATOM 2968 C SER B 386 10.554 70.875 -22.532 1.00 0.00
ATOM 2969 O SER B 386 10.781 71.899 -21.850 1.00 0.00
ATOM 2970 OXT SER B 386 10.967 70.744 -23.728 1.00 0.00