Chain ID

The PDB gives no guidelines for the use of chain identifiers, other than that one is encouraged to use certain characters:

Only non-control ASCII characters, as well as the space and end-of-line indicator, appear in a PDB coordinate entry file. Namely:
abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ
1234567890
` - = [ ] \ ; ' , . / ~ ! @ # $ % ^ & * ( ) _ + { } | : " < > ?
We discourage use of punctuation characters in the place of alphanumeric
characters. The space, and end-of-line:. The end-of-line indicator is
system-specific. Unix uses a line feed character; other systems may use
a carriage return followed by a line feed.

However, a few rules-of-thumb have emerged over the years:

1. If it is one chain in biology it should have one chain-id in the PDB file
2. Chain-ids are preferably given as either logical abbreviations (E and I for Enzyme and Inhibitor; or L and H for Light and Heavy chain), or in increasing alphabetical order (A, B, C, D, etc).
3. If there is no need for the use of chain identifiers it was habit in the past not to use any. Lately, the chain-id A is used for such cases.

For the latter it is a pity that abc...xyz come before ABC...XYZ in the ASCII code listed above. Because we normally start with the capitals and use numericals and lower case characters "in case of emergency" only, which for the lower case characters breaks rule of thumb number 2.

EU name: 1K7C

1K7C

JRNL        AUTH   A.MOLGAARD,S.LARSEN
JRNL        TITL   A BRANCHED N-LINKED GLYCAN AT ATOMIC RESOLUTION IN
JRNL        TITL 2 THE 1.12 A STRUCTURE OF RHAMNOGALACTURONAN
JRNL        TITL 3 ACETYLESTERASE
JRNL        REF    ACTA CRYSTALLOGR., SECT.D     V.  58   111 2002
JRNL        REFN   ASTM ABCRE6  DK ISSN 0907-4449

In the file 1k7c.pdb the protein has chain-id A; one of the sugars too. Most other sugars have chain-id B, but the sulphates and the waters have no chain-id at all.

Additionally, it is somewhat funny to see that the sugars are fully bound by symmetry related molecules. Normally the presence of sugars make crystallisation difficult, but in this case, it seems the sugars were important for forming the crystals.

The structure of 1k7c. The very thin lines represent a layer of 10 Ångström of residues (etcetera) in symmetry related molecules. The waters were not shown for clarity.

The same situation, but now rotating to see things better...

The structure again. The red NAG has chain-id A, just like the protein it is bound to. The yellow NAG, also bound to the protein, has chain-id B...

1E4M 1MYP

In 1e4m everything (amino acids, PO₄, Zn, has chain-id M, but the waters have chain-id X. In 1MYP the sugars have a different chain-id from the residues they are covalently bound to.

EU name: 1HTR

1HTR

REMARK   1 REFERENCE 1                                                  1HTR  15
REMARK   1  AUTH   P.K.IVANOV,M.CHERNAIA,A.E.GUSTCHINA,I.V.PECHIK,      1HTR  16
REMARK   1  AUTH 2 S.V.NIKONOV,N.I.TARASOVA                             1HTR  17
REMARK   1  TITL   ISOLATION, CRYSTALLIZATION AND PRELIMINARY X-RAY     1HTR  18
REMARK   1  TITL 2 DIFFRACTION DATA OF HUMAN PROGASTRICSIN              1HTR  19
REMARK   1  REF    BIOCHIM.BIOPHYS.ACTA          V.1040   308 1990      1HTR  20
REMARK   1  REFN   ASTM BBACAQ  NE ISSN 0006-3002                 0113  1HTR  21

This file contains one very intruiging water.

In 1htr none of the water molecules has a chain-id, except for one that has chain-id B. Indicated as a red-dotted yellow sphere.

And here the structure is rotating around. No matter how I look at it the water with chain-id B remains an intruiging mistery.