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PDBFixer fixes problems in PDB files
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Histidines created with Hs at HD1 and HE1 #209

Closed tdudgeon closed 3 years ago

tdudgeon commented 3 years ago

When adding hydrogens I'm finding that histidines are not be handled correctly.

pdbfixer protein.pdb --add-atoms=all --ph=7

Before:

ATOM    303  N   HIS A  41      14.444  -7.662  22.209  1.00 14.91           N  
ATOM    304  CA  HIS A  41      13.763  -7.017  23.355  1.00 16.16           C  
ATOM    305  C   HIS A  41      12.537  -7.853  23.762  1.00 16.81           C  
ATOM    306  O   HIS A  41      11.970  -7.560  24.818  1.00 16.49           O  
ATOM    307  CB  HIS A  41      13.531  -5.540  23.082  1.00 16.04           C  
ATOM    308  CG  HIS A  41      12.405  -5.273  22.162  1.00 16.15           C  
ATOM    309  CD2 HIS A  41      11.094  -5.553  22.274  1.00 17.21           C  
ATOM    310  ND1 HIS A  41      12.569  -4.556  20.983  1.00 19.09           N  
ATOM    311  CE1 HIS A  41      11.384  -4.393  20.422  1.00 14.71           C  
ATOM    312  NE2 HIS A  41      10.479  -5.050  21.149  1.00 19.19           N

After:

ATOM    605  N   HIS A  41      14.444  -7.662  22.209  1.00  0.00           N  
ATOM    606  H   HIS A  41      14.806  -6.791  21.491  1.00  0.00           H  
ATOM    607  CA  HIS A  41      13.763  -7.017  23.355  1.00  0.00           C  
ATOM    608  HA  HIS A  41      14.435  -7.019  24.335  1.00  0.00           H  
ATOM    609  C   HIS A  41      12.537  -7.853  23.762  1.00  0.00           C  
ATOM    610  O   HIS A  41      11.970  -7.560  24.818  1.00  0.00           O  
ATOM    611  CB  HIS A  41      13.531  -5.540  23.082  1.00  0.00           C  
ATOM    612  HB2 HIS A  41      12.992  -5.092  24.050  1.00  0.00           H  
ATOM    613  HB3 HIS A  41      14.443  -4.817  22.822  1.00  0.00           H  
ATOM    614  CG  HIS A  41      12.405  -5.273  22.162  1.00  0.00           C  
ATOM    615  CD2 HIS A  41      11.094  -5.553  22.274  1.00  0.00           C  
ATOM    616  HD2 HIS A  41      10.264  -5.440  23.117  1.00  0.00           H  
ATOM    617  ND1 HIS A  41      12.569  -4.556  20.983  1.00  0.00           N  
ATOM    618  HD1 HIS A  41      13.396  -3.749  20.719  1.00  0.00           H  
ATOM    619  CE1 HIS A  41      11.384  -4.393  20.422  1.00  0.00           C  
ATOM    620  HE1 HIS A  41      10.868  -3.330  20.637  1.00  0.00           H  
ATOM    621  NE2 HIS A  41      10.479  -5.050  21.149  1.00  0.00           N

Note how HD2 and HE1 are present. This would correspond to the charged form (HIP - see http://ambermd.org/Questions/HIS.html) that would not be expected at pH 7.

peastman commented 3 years ago

HD2 and HE1 are always present, regardless of the form. HD1 and HE2 are the variable ones. The above file has HD1 but not HE2, corresponding to the HID form.

tdudgeon commented 3 years ago

Sorry, got mixed up on this. I'm sure I was seeing H on both Ns, but that is not the case.