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
UandVat 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 usesA,B,C, andD, while CU306 only usesAandB:
...
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
...
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.