Hello!
I have a crystal structure of an enzyme (HisRS) which is tetramer. The residues between 185 to 228 are missing for all chains. How to manage this issue?
If I load the pdb file as it is then it forms a bond between the residue 185 and 228 which is unnatural. A part of the pdb file showing the coordinate of residue 185 and residue 228 is shown as follows:
ATOM 1793 N LEU A 185 2.488 44.813 7.408 1.00 77.39 N
ATOM 1794 CA LEU A 185 3.537 43.802 7.492 1.00 80.42 C
ATOM 1795 C LEU A 185 4.779 44.212 6.665 1.00 82.35 C
ATOM 1796 O LEU A 185 5.855 44.529 7.215 1.00 83.14 O
ATOM 1797 CB LEU A 185 2.993 42.429 7.043 1.00 79.48 C
ATOM 1798 H LEU A 185 1.645 44.592 6.981 1.00 0.00 H
ATOM 1799 N TYR A 228 -12.077 46.733 12.305 1.00 60.84 N
ATOM 1800 CA TYR A 228 -12.163 46.419 10.872 1.00 61.23 C
ATOM 1801 C TYR A 228 -13.202 45.304 10.589 1.00 61.67 C
ATOM 1802 O TYR A 228 -13.126 44.609 9.561 1.00 61.76 O
ATOM 1803 CB TYR A 228 -10.757 46.026 10.324 1.00 60.27 C
ATOM 1804 H TYR A 228 -12.893 46.851 12.828 1.00 0.00 H
If I add ‘TER’ in between the coordinates of residue 185 and coordinate of residue 228 then leap consider the 185 residue as C-terminal residue and 228 residue as N-terminal residue and creates one additional positive charge for the amino croup of 185 residue and a negative charge for the carboxylic acid group of 228 residue. A part of the pdb file showing the coordinate of residue 185 and residue 228 in the modified pdb file is shown as follows:
ATOM 1793 N LEU A 185 2.488 44.813 7.408 1.00 77.39 N
ATOM 1794 CA LEU A 185 3.537 43.802 7.492 1.00 80.42 C
ATOM 1795 C LEU A 185 4.779 44.212 6.665 1.00 82.35 C
ATOM 1796 O LEU A 185 5.855 44.529 7.215 1.00 83.14 O
ATOM 1797 CB LEU A 185 2.993 42.429 7.043 1.00 79.48 C
ATOM 1798 H LEU A 185 1.645 44.592 6.981 1.00 0.00 H
TER
ATOM 1799 N TYR A 228 -12.077 46.733 12.305 1.00 60.84 N
ATOM 1800 CA TYR A 228 -12.163 46.419 10.872 1.00 61.23 C
ATOM 1801 C TYR A 228 -13.202 45.304 10.589 1.00 61.67 C
ATOM 1802 O TYR A 228 -13.126 44.609 9.561 1.00 61.76 O
ATOM 1803 CB TYR A 228 -10.757 46.026 10.324 1.00 60.27 C
Now I want to make the carboxylic acid group (-COO-) of 185 residue and amino group of (-NH3+) residue 228 as neutral. How to do this? I also want to know in general what is used in such cases.
With best regards
Sindrila
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Received on Tue Jun 14 2011 - 23:00:03 PDT
