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 '''never<ref name="cacho">An exception is Ca318 in [[3gzt]], which is assigned chain X, a disaccharide. Ca318 is 44 Å from the disaccharide, but only 26 Å from the nearest protein (chain Q).</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]]).

# When protein or nucleic acid is present, ligands and water bound to carbohydrate are '''never<ref name="cacho">An exception is Ca318 in [[3gzt]], which is assigned chain ID X. Chain X is a disaccharide. Ca318 is 44 Å from the disaccharide, but only 26 Å from the nearest protein (chain Q).</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. Traditionally deemed ligands, '''dipeptides are assigned the ID of the polymer chain to which they are bound'''. Dipeptide examples are [[2cyh]] and [[1dpp]]; tripeptide: [[4q1l|4q1L]]. This is correctly 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 assigned unique chain IDs.

Chains and Chain IDs: Difference between revisions

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@@ Line 27: / Line 27: @@
 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 '''never<ref name="cacho">An exception is Ca318 in [[3gzt]], which is assigned chain X, a disaccharide. Ca318 is 44 &Aring; from the disaccharide, but only 26 &Aring; from the nearest protein (chain Q).</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]]).
+# When protein or nucleic acid is present, ligands and water bound to carbohydrate are '''never<ref name="cacho">An exception is Ca318 in [[3gzt]], which is assigned chain ID X. Chain X is a disaccharide. Ca318 is 44 &Aring; from the disaccharide, but only 26 &Aring; from the nearest protein (chain Q).</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. Traditionally deemed ligands, '''dipeptides are assigned the ID of the polymer chain to which they are bound'''. Dipeptide examples are [[2cyh]] and [[1dpp]]; tripeptide: [[4q1l|4q1L]]. This is correctly 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 assigned unique chain IDs.