Chains and Chain IDs: Difference between revisions

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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:

# When protein or nucleic acid is present, ligands and water bound to carbohydrate are '''almost never<ref name="cacho">An exception is Ca318 in [[3gzt]], which is assigned chain ID X. Chain X is a disaccharide. In the asymmetric unit, Ca318 is 44 Å from the disaccharide, but only 26 Å from the nearest protein (chain Q). In Biomolecule 4, it is 2.6 Å from sidechain oxygens of Asp231 in chain B, and in the vicinity of two other chain B Asp.</ref> assigned the chain ID of that carbohydrate''', but are given the chain ID of the nearest protein/nucleic acid, even when it is >5 Å away (examples: [[7lkc|7LKC]], [[7dc4]], [[8g82]]). When the structure is carbohydrate without any protein or nucleic acid, only then are ligands and water given the chain ID of the nearest carbohydrate (examples: [[1c58]], [[2kqo]]).

# Although dinucleotides and disaccharides are assigned unique chain IDs, '''dipeptides are not supposed to be assigned unique chain IDs. However, this policy has not been followed consistently.''' A search at RCSB for ''Polymer Entity Sequence Length'' = 2 and ''Polymer Entity Type'' is Protein and Return ''Polymer Entities'' finds 59 hits (April, 2025), where dipeptides were given unique author-assigned chain IDS (in both PDB format and mmCIF format files). Traditionally deemed ligands, dipeptides are supposed to be assigned the same chain ID as the polymer chain to which they are bound. Dipeptide examples are [[2cyh]] and [[1dpp]]; tripeptide: [[4q1l|4q1L]~~]. This policy is documented at the wwPDB in [https://www.wwpdb.org/documentation/procedure#toc_3 3. Polymer sequences and sequence database reference assignment~~]. Tripeptides and longer oligopeptides are supposed to be assigned unique chain IDs. When a dipeptide is not assigned a unique chain ID, it has no SEQRES and cannot be found by a search for polymer length at RCSB (April, 2025).

# Although dinucleotides and disaccharides are assigned unique chain IDs, '''dipeptides are not supposed to be assigned unique chain IDs.''' This policy is documented at the wwPDB in [https://www.wwpdb.org/documentation/procedure#toc_3 3. Polymer sequences and sequence database reference assignment]. '''However, this policy has not been followed consistently.''' A search at RCSB for ''Polymer Entity Sequence Length'' = 2 and ''Polymer Entity Type'' is Protein and Return ''Polymer Entities'' finds 59 hits (April, 2025), where dipeptides were given unique author-assigned chain IDS (in both PDB format and mmCIF format files). Traditionally deemed ligands, dipeptides are supposed to be assigned the same chain ID as the polymer chain to which they are bound. Dipeptide examples are [[2cyh]] and [[1dpp]]; tripeptide: [[4q1l|4q1L]]. Tripeptides and longer oligopeptides are supposed to be assigned unique chain IDs. When a dipeptide is not assigned a unique chain ID, it has no SEQRES and cannot be found by a search for polymer length at RCSB (April, 2025).

===Author vs. wwPDB Chain IDs===

Chains and Chain IDs: Difference between revisions

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 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:
 # When protein or nucleic acid is present, ligands and water bound to carbohydrate are '''almost never<ref name="cacho">An exception is Ca318 in [[3gzt]], which is assigned chain ID X. Chain X is a disaccharide. In the asymmetric unit, Ca318 is 44 &Aring; from the disaccharide, but only 26 &Aring; from the nearest protein (chain Q). In Biomolecule 4, it is 2.6 &Aring; from sidechain oxygens of Asp231 in chain B, and in the vicinity of two other chain B Asp.</ref>  assigned the chain ID of that carbohydrate''', but are given the chain ID of the nearest protein/nucleic acid, even when it is >5 &Aring; away (examples: [[7lkc|7LKC]], [[7dc4]], [[8g82]]). When the structure is carbohydrate without any protein or nucleic acid, only then are ligands and water given the chain ID of the nearest carbohydrate (examples: [[1c58]], [[2kqo]]).
-# Although dinucleotides and disaccharides are assigned unique chain IDs, '''dipeptides are not supposed to be assigned unique chain IDs. However, this policy has not been followed consistently.''' A search at RCSB for ''Polymer Entity Sequence Length'' = 2 and ''Polymer Entity Type'' is Protein and Return ''Polymer Entities'' finds 59 hits (April, 2025), where dipeptides were given unique author-assigned chain IDS (in both PDB format and mmCIF format files). Traditionally deemed ligands, dipeptides are supposed to be assigned the same chain ID as the polymer chain to which they are bound. Dipeptide examples are [[2cyh]] and [[1dpp]]; tripeptide: [[4q1l|4q1L]]. This policy is documented at the wwPDB in [https://www.wwpdb.org/documentation/procedure#toc_3 3. Polymer sequences and sequence database reference assignment]. Tripeptides and longer oligopeptides are supposed to be assigned unique chain IDs. When a dipeptide is not assigned a unique chain ID, it has no SEQRES and cannot be found by a search for polymer length at RCSB (April, 2025).
+# Although dinucleotides and disaccharides are assigned unique chain IDs, '''dipeptides are not supposed to be assigned unique chain IDs.'''  This policy is documented at the wwPDB in [https://www.wwpdb.org/documentation/procedure#toc_3 3. Polymer sequences and sequence database reference assignment]. '''However, this policy has not been followed consistently.''' A search at RCSB for ''Polymer Entity Sequence Length'' = 2 and ''Polymer Entity Type'' is Protein and Return ''Polymer Entities'' finds 59 hits (April, 2025), where dipeptides were given unique author-assigned chain IDS (in both PDB format and mmCIF format files). Traditionally deemed ligands, dipeptides are supposed to be assigned the same chain ID as the polymer chain to which they are bound. Dipeptide examples are [[2cyh]] and [[1dpp]]; tripeptide: [[4q1l|4q1L]]. Tripeptides and longer oligopeptides are supposed to be assigned unique chain IDs. When a dipeptide is not assigned a unique chain ID, it has no SEQRES and cannot be found by a search for polymer length at RCSB (April, 2025).
 ===Author vs. wwPDB Chain IDs===