On Tue, Jun 14, 2011 at 11:57 PM, Sindrila Dutta banik <
sindrila.duttabanik.yahoo.com> wrote:
> 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.
>
You can use terminal caps. For instance, ACE for the C-terminal end and
NME/NHE for the N-terminal end. These are neutral.
HTH,
Jason
>
> With best regards
> Sindrila
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jun 17 2011 - 09:30:05 PDT
