Meaning of shared alternate location indicator between residues in PDB format
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8 months ago
Pshenichnaya ▴ 10

This is a question on the PDB ALTLOC field (and associated MMCIF _atom_site.label_alt_id field). On the RCSB guideline for PDB files (https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html), it says:

AltLoc is the place holder to indicate alternate conformation. The alternate conformation can be in the entire polymer chain, or several residues or partial residue (several atoms within one residue). If an atom is provided in more than one position, then a non-blank alternate location indicator must be used for each of the atomic positions. Within a residue, all atoms that are associated with each other in a given conformation are assigned the same alternate position indicator. There are two ways of representing alternate conformation- either at atom level or at residue level (see examples).

Unfortunately, this says nothing about atom associates between residues - if the same indicator only associates atoms within a residue, then what about between residues or between chains? For example, 1ZIR (https://www.rcsb.org/structure/1ZIR) has AltLoc indicators from A to V, and indicators A and B are across many residues, including as GLN1100 and PHE1115. Indicators U and V only occur on MET1135.

...  
ATOM    886  CG AGLN A1100      21.330   4.535  56.779  0.55 18.00           C  
ATOM    887  CG BGLN A1100      20.745   4.030  56.827  0.45 19.40           C  
ATOM    888  CD AGLN A1100      20.853   3.813  58.017  0.55 17.45           C  
ATOM    889  CD BGLN A1100      19.280   4.381  56.613  0.45 30.19           C  
ATOM    890  OE1AGLN A1100      20.292   2.717  57.945  0.55 19.03           O  
ATOM    891  OE1BGLN A1100      18.727   4.146  55.535  0.45 31.64           O  
ATOM    892  NE2AGLN A1100      21.062   4.411  59.188  0.55 21.04           N  
ATOM    893  NE2BGLN A1100      18.632   4.930  57.630  0.45 26.03           N  
...  
ATOM   1012  N  APHE A1115      15.322   6.363  48.325  0.55 19.30           N  
ATOM   1013  N  BPHE A1115      15.385   6.516  48.110  0.45 12.49           N  
ATOM   1014  CA APHE A1115      15.480   5.433  49.473  0.55 15.10           C  
ATOM   1015  CA BPHE A1115      16.116   5.965  49.240  0.45 10.22           C  
ATOM   1016  C  APHE A1115      15.206   5.993  50.847  0.55 23.49           C  
ATOM   1017  C  BPHE A1115      16.492   6.894  50.391  0.45 11.22           C  
ATOM   1018  O  APHE A1115      14.644   7.089  50.972  0.55 25.14           O  
ATOM   1019  O  BPHE A1115      16.601   6.397  51.529  0.45 10.92           O  
ATOM   1020  CB APHE A1115      16.896   4.852  49.315  0.55 16.67           C  
ATOM   1021  CB BPHE A1115      17.431   5.365  48.705  0.45 10.63           C  
ATOM   1022  CG APHE A1115      16.941   4.032  48.019  0.55 16.38           C  
ATOM   1023  CG BPHE A1115      17.316   4.214  47.725  0.45 12.50           C  
ATOM   1024  CD1APHE A1115      16.125   2.920  47.877  0.55 16.76           C  
ATOM   1025  CD1BPHE A1115      16.462   3.145  47.955  0.45 15.81           C  
ATOM   1026  CD2APHE A1115      17.777   4.373  46.982  0.55 13.67           C  
ATOM   1027  CD2BPHE A1115      18.077   4.194  46.567  0.45 15.00           C  
ATOM   1028  CE1APHE A1115      16.155   2.162  46.715  0.55 15.61           C  
ATOM   1029  CE1BPHE A1115      16.379   2.094  47.058  0.45 17.92           C  
ATOM   1030  CE2APHE A1115      17.820   3.624  45.822  0.55 15.40           C  
ATOM   1031  CE2BPHE A1115      18.009   3.150  45.665  0.45 16.55           C  
ATOM   1032  CZ APHE A1115      17.008   2.513  45.685  0.55 16.02           C  
ATOM   1033  CZ BPHE A1115      17.163   2.087  45.919  0.45 15.52           C  
...  
ATOM   1252  CB UMET A1135      22.381  14.143  36.653  0.57 14.70           C  
ATOM   1253  CB VMET A1135      22.363  14.175  36.699  0.43 16.47           C  
ATOM   1254  CG UMET A1135      23.449  15.212  36.809  0.57 21.67           C  
ATOM   1255  CG VMET A1135      23.585  15.074  36.664  0.43 19.74           C  
ATOM   1256  SD UMET A1135      23.553  16.378  35.435  0.57 28.73           S  
ATOM   1257  SD VMET A1135      23.762  16.131  38.116  0.43 25.91           S  
ATOM   1258  CE UMET A1135      22.716  17.796  36.150  0.57 31.49           C  
ATOM   1259  CE VMET A1135      25.076  17.215  37.550  0.43 25.03           C  
...  
  • Are the atoms in AltLoc A of GLN1100 part of the same conformation as AltLoc A of PHE1115? Or is the indicator symbol essentially arbitrary between residues or chains?
  • If the indicator symbol is arbitrary between residues and chains, then why does MET1135 use U and V at all?
  • If the indicator symbol is NOT arbitrary between residues and chains, then what does it mean when some residues have more AltLoc indicators than others? E.g. for 1V6P, CU302 uses A, B, C, and D, while CU306 only uses A and B:
...  
HETATM 1188 CU  A CU A 302     -11.178  -1.681  33.175  0.57  6.40          CU  
ANISOU 1188 CU  A CU A 302      642    938    852   -235     10   -154      CU  
HETATM 1189 CU  B CU A 302     -11.588  -1.317  32.695  0.16  7.67          CU  
ANISOU 1189 CU  B CU A 302     1049   1066    800   -307   -171    142      CU  
HETATM 1190 CU  C CU A 302     -11.090  -2.361  32.713  0.09  9.67          CU  
ANISOU 1190 CU  C CU A 302      986   1535   1156      5    211    541      CU  
HETATM 1191 CU  D CU A 302     -10.005  -2.562  33.178  0.18 26.63          CU  
ANISOU 1191 CU  D CU A 302     2370   1509   6240    -14   1516   -314      CU  
HETATM 1192 CU    CU A 303      -1.662  -7.054  26.211  0.77  7.97          CU  
ANISOU 1192 CU    CU A 303     1039   1014    977     10    208   -175      CU  
HETATM 1193 CU    CU A 304      -7.712   2.824  48.599  0.11  9.65          CU  
ANISOU 1193 CU    CU A 304      624   1334   1708     78    172    445      CU  
HETATM 1194 CU    CU A 305      -8.294  -9.680  28.531  0.45  9.12          CU  
ANISOU 1194 CU    CU A 305     1092   1476    896    192     -9    166      CU  
HETATM 1195 CU  A CU A 306      -5.686  21.411  41.663  0.38 18.87          CU  
ANISOU 1195 CU  A CU A 306     2678   1596   2897    822   1341     63      CU  
HETATM 1196 CU  B CU A 306      -6.646  20.748  41.563  0.22 15.70          CU  
ANISOU 1196 CU  B CU A 306     2172   1032   2762   -451   1689   -542      CU  
HETATM 1197 CU    CU A 307      -0.523  -5.806  23.644  0.13  6.20          CU  
ANISOU 1197 CU    CU A 307      761   1025    569    142    119    -53      CU  
...  
pdb atomic-coordinates alternate-location • 286 views
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My guess is that it's arbitrary, because the person who builds the model knows only (from experimental data) an average of electron densities of all conformations, so they couldn't tell that one altloc corresponds to another altloc 15 residues away.

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