Nomenclature Details

[HanneWhitt]

I have some questions on the format of chain IDs in the [ID] field.

Question 1: 'chain_number'
I understand from the documentation that ids of format e.g 1VBK_1_A have the following parts:

<pdb_id>_<chain_number>_<chain_id>

However, I do not understand the meaning of the 'chain_number' field. Is this a simple index of the chain in the pdb file, or a reference to the model in multi-model PDB files?

Question 2. Last digit, alternative format
Some IDs do not have this format and instead look like this:

2EUL_d2euld1
1H4V_d1h4vb1
1C4K_d1c4ka2
1V5F_d1v5fa1

I understand that:

1. The first characters are the pdb_id
2. The 'd' means domain
3. The next few characters represent the domain

However I do not understand the meaning of the final digit ('1' or '2') in the above examples. What does this signify?

Many thanks!

[alquraishi]

Re question 1: the chain number is the identifier coming from the original mmCIF file and has nothing to do with multi-model files. In the latter case the first model is retained and the rest are ignored.

Re question 2: these identifiers are coming from ASTRAL. See here.

Hope this helps!