How to generate constraints of active sites from a pdb file of an enzyme

[Anonymous]

Greetings, everyone. I got the pdb file of an enzyme, but I don’t know how to write the constraints of its active sites.
Could anyone help me solve this problem?
Much appreciate it.

When I open the pdb file with txteditor, I can see coordinates as:
ATOM 1 N HIS A 27 10.218 -30.379 -16.292 1.00 12.31 N
ATOM 2 CA HIS A 27 10.486 -29.045 -15.829 1.00 12.44 C
ATOM 3 C HIS A 27 11.803 -28.537 -16.417 1.00 12.46 C
ATOM 4 O HIS A 27 11.912 -27.351 -16.894 1.00 11.54 O
ATOM 5 CB HIS A 27 10.509 -29.082 -14.280 1.00 10.82 C
ATOM 6 CG HIS A 27 10.402 -27.733 -13.630 1.00 11.50 C
ATOM 7 CD2 HIS A 27 10.266 -26.472 -14.145 1.00 12.66 C
ATOM 8 ND1 HIS A 27 10.504 -27.583 -12.255 1.00 13.07 N
ATOM 9 CE1 HIS A 27 10.391 -26.290 -11.951 1.00 14.54 C
ATOM 10 NE2 HIS A 27 10.244 -25.612 -13.074 1.00 11.43 N
TER 11 HIS A 27
ATOM 12 N HIS A 82 15.205 -20.416 -13.135 1.00 12.48 N
ATOM 13 CA HIS A 82 15.416 -21.885 -13.107 1.00 13.11 C
ATOM 14 C HIS A 82 16.910 -22.184 -12.930 1.00 12.05 C
ATOM 15 O HIS A 82 17.251 -23.177 -12.288 1.00 13.17 O
ATOM 16 CB HIS A 82 14.874 -22.584 -14.379 1.00 13.33 C
ATOM 17 CG HIS A 82 13.390 -22.639 -14.405 1.00 12.06 C
ATOM 18 CD2 HIS A 82 12.512 -23.596 -14.011 1.00 12.97 C
ATOM 19 ND1 HIS A 82 12.649 -21.563 -14.827 1.00 10.57 N
ATOM 20 CE1 HIS A 82 11.356 -21.860 -14.688 1.00 14.15 C
ATOM 21 NE2 HIS A 82 11.257 -23.079 -14.182 1.00 13.12 N
TER 22 HIS A 82

How can I determine the distance, angles and dihedrals between the two residues?

[Anonymous]

Hi Albert !
I use pymol for calculating the distance, angles and dihedrals between the two residues.
To know more about constraints go to https://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/file_constraints.html

[Anonymous]

Hi Albert,
In addition, if you know python, you can look into using PyRosetta and the iPython shell to do it in code.

[Anonymous]

That’s just what I’ve been looking for. Thank you very much!

[Author]

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