Chains and Chain IDs: Difference between revisions

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In the [[atomic coordinate file]]s maintained by the [[wwPDB]] ([[PDB files]]), each polymer chain is given an ID, or chain "name". In the legacy [[Atomic_coordinate_file#PDB_Data_Format|PDB data format]], chain IDs are a single letter or numeral (A-Z, a-z, 0-9), which limits the number of chains to 62. In the newer [[Atomic_coordinate_file#mmCIF_Data_Format|mmCIF data format]] (also called PDBx), chain IDs can be [https://mmcif.wwpdb.org/docs/large-pdbx-examples/index.html up to 4 letters or numerals], so the number of chains in a single structure is essentially unlimited (>10 million chains/structure could be accommodated by 4-character chain IDs).

===~~Carbohydrate and Non-Polymer~~ Chain IDs===

===Oligosaccharide Chain IDs===

An idiosyncracy of PDB files is that not only polymer chains, but all components in the structure model are assigned chain IDs, including carbohydrates (regardless of whether covalently-linked), ligands, metal ions, and water. The assignment of unique ~~names~~ to disaccharides and oligosaccharides began with the [https://www.wwpdb.org/documentation/remediation 2020 wwPDB Remediation of Carbohydrates].

The assignment of unique chain IDs to disaccharides and oligosaccharides began with the [https://www.wwpdb.org/documentation/remediation 2020 wwPDB Remediation of Carbohydrates]. Notably, '''monomeric''' nucleotides and amino acids (not part of a polymeric chain) and monosaccharides are assigned the chain ID of the '''nearest protein or nucleic acid''', while '''multimeric''' di- or oligo-nucleotides, and di- or oligosaccharides are given '''unique''' chain IDs. See item 2 below for the special case of dipeptides vs. tri- / oligo-peptides.

Notably, '''monomeric''' nucleotides and amino acids (not part of a polymeric chain) and monosaccharides are assigned the chain ID of the '''nearest protein or nucleic acid''', while '''multimeric''' di- or oligo-nucleotides, and di- or oligosaccharides are given '''unique''' chain IDs. See item 2 below for the special case of dipeptides vs. tri- / oligo-peptides.

The procedure for assigning chain IDs is specified in the wwPDB Procedures section [https://www.wwpdb.org/documentation/procedure#toc_6 6. Chain ID assignment]. In February, 2025 that document needs two corrections in order to agree with actual wwPDB practice:

Chains and Chain IDs: Difference between revisions

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 In the [[atomic coordinate file]]s maintained by the [[wwPDB]] ([[PDB files]]), each polymer chain is given an ID, or chain "name". In the legacy [[Atomic_coordinate_file#PDB_Data_Format|PDB data format]], chain IDs are a single letter or numeral (A-Z, a-z, 0-9), which limits the number of chains to 62. In the newer [[Atomic_coordinate_file#mmCIF_Data_Format|mmCIF data format]] (also called PDBx), chain IDs can be [https://mmcif.wwpdb.org/docs/large-pdbx-examples/index.html up to 4 letters or numerals], so the number of chains in a single structure is essentially unlimited (>10 million chains/structure could be accommodated by 4-character chain IDs).
-===Carbohydrate and Non-Polymer Chain IDs===
+===Oligosaccharide Chain IDs===
-An idiosyncracy of PDB files is that not only polymer chains, but all components in the structure model are assigned chain IDs, including carbohydrates (regardless of whether covalently-linked), ligands, metal ions, and water. The assignment of unique names to disaccharides and oligosaccharides began with the [https://www.wwpdb.org/documentation/remediation 2020 wwPDB Remediation of Carbohydrates].
+The assignment of unique chain IDs to disaccharides and oligosaccharides began with the [https://www.wwpdb.org/documentation/remediation 2020 wwPDB Remediation of Carbohydrates]. Notably, '''monomeric''' nucleotides and amino acids (not part of a polymeric chain) and monosaccharides are assigned the chain ID of the '''nearest protein or nucleic acid''', while '''multimeric''' di- or oligo-nucleotides, and di- or oligosaccharides are given '''unique''' chain IDs. See item 2 below for the special case of dipeptides vs. tri- / oligo-peptides.
-Notably, '''monomeric''' nucleotides and amino acids (not part of a polymeric chain) and monosaccharides are assigned the chain ID of the '''nearest protein or nucleic acid''', while '''multimeric''' di- or oligo-nucleotides, and di- or oligosaccharides are given '''unique''' chain IDs. See item 2 below for the special case of dipeptides vs. tri- / oligo-peptides.
 The procedure for assigning chain IDs is specified in the wwPDB Procedures section [https://www.wwpdb.org/documentation/procedure#toc_6 6. Chain ID assignment]. In February, 2025 that document needs two corrections in order to agree with actual wwPDB practice: