Chains and Chain IDs: Difference between revisions

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===Oligosaccharide Chain IDs===

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.

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. N-linked glycans are likely underrepresented in the PDB due to microheterogeneity and their flexibility<ref>PMID: 40645091</ref>.

===Chain ID Assignment Policies===

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===AlphaFold3 Chain IDs===

The [https://alphafoldserver.com AlphaFold Server], which in 2025 uses AlphaFold3<ref name="af3">PMID: 38718835</ref>, predicts complexes with multiple chains of protein and/or nucleic acid, plus a limited set of ligands, and metal ions, and a wide range of post-translational modifications of amino acids and chemical modifications of nucleotides. Predicted models are available in '''mmCIF''' format only (not PDB format, although the mmCIF files can be [[Converting AlphaFold3 CIF to PDB|easily converted to PDB format]]). Consistent with the chain ID assignment policies of the wwPDB for mmCIF files, every entity is assigned a unique chain ID, including polymer chains, ligands, metal ions, and glycans including oligo- and monosaccharides. The following three examples are provided by the Server.

The [https://alphafoldserver.com AlphaFold Server], which in 2025 uses AlphaFold3<ref name="af3">PMID: 38718835</ref>, predicts complexes with multiple chains of protein and/or nucleic acid, plus a limited set of ligands, and metal ions, and a wide range of post-translational modifications of amino acids and chemical modifications of nucleotides (see [[How to predict structures with AlphaFold]]). Predicted models are available in '''mmCIF''' format only (not PDB format, although the mmCIF files can be [[Converting AlphaFold3 CIF to PDB|easily converted to PDB format]]). Consistent with the chain ID assignment policies of the wwPDB for mmCIF files, every entity is assigned a unique chain ID, including polymer chains, ligands, metal ions, and glycans including oligo- and monosaccharides. The following three examples are provided by the Server.

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<td>

1 ID total:

:Protein,Zn++,Monomeric mannose glycoconjugates: A.

:Protein, Zn++, Monomeric mannose glycoconjugates: A.

</td>

<td>

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<td>

3 IDs total:

:Protein,Ca++,Na+: A.

:Protein, Ca++, Na+: A.

:DNA: B, C.

</td>

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</td>

<td>

The 2.4 Å X-ray model has 85 amino acid sidechains missing distal atoms, including 50 charged residues, and is completely missing a small loop of 4 residues that includes one positive charge. These missing atoms are all present in the AlphaFold3-predicted model.

</td>

Chains and Chain IDs: Difference between revisions

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@@ Line 24: / Line 24: @@
 ===Oligosaccharide Chain IDs===
-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.
+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. N-linked glycans are likely underrepresented in the PDB due to microheterogeneity and their flexibility<ref>PMID: 40645091</ref>.
 ===Chain ID Assignment Policies===
@@ Line 226: / Line 226: @@
 ===AlphaFold3 Chain IDs===
-The [https://alphafoldserver.com AlphaFold Server], which in 2025 uses AlphaFold3<ref name="af3">PMID: 38718835</ref>, predicts complexes with multiple chains of protein and/or nucleic acid, plus a limited set of ligands, and metal ions, and a wide range of post-translational modifications of amino acids and chemical modifications of nucleotides. Predicted models are available in '''mmCIF''' format only (not PDB format, although the mmCIF files can be [[Converting AlphaFold3 CIF to PDB|easily converted to PDB format]]). Consistent with the chain ID assignment policies of the wwPDB for mmCIF files, every entity is assigned a unique chain ID, including polymer chains, ligands, metal ions, and glycans including oligo- and monosaccharides. The following three examples are provided by the Server.
+The [https://alphafoldserver.com AlphaFold Server], which in 2025 uses AlphaFold3<ref name="af3">PMID: 38718835</ref>, predicts complexes with multiple chains of protein and/or nucleic acid, plus a limited set of ligands, and metal ions, and a wide range of post-translational modifications of amino acids and chemical modifications of nucleotides (see [[How to predict structures with AlphaFold]]). Predicted models are available in '''mmCIF''' format only (not PDB format, although the mmCIF files can be [[Converting AlphaFold3 CIF to PDB|easily converted to PDB format]]). Consistent with the chain ID assignment policies of the wwPDB for mmCIF files, every entity is assigned a unique chain ID, including polymer chains, ligands, metal ions, and glycans including oligo- and monosaccharides. The following three examples are provided by the Server.
 <table class="wikitable">
@@ Line 257: / Line 257: @@
      <td>
 ID total:
-:Protein,Zn++,Monomeric mannose glycoconjugates: <b>A</b>.
+:Protein, Zn++, Monomeric mannose glycoconjugates: <b>A</b>.
      </td>
      <td>
@@ Line 279: / Line 279: @@
      <td>
 IDs total:
-:Protein,Ca++,Na+: <b>A</b>.
+:Protein, Ca++, Na+: <b>A</b>.
 :DNA: <b>B, C</b>.
      </td>
@@ Line 291: / Line 291: @@
      </td>
      <td>
+The 2.4 &Aring; X-ray model has 85 amino acid sidechains missing distal atoms, including 50 charged residues, and is completely missing a small loop of 4 residues that includes one positive charge. These missing atoms are all present in the AlphaFold3-predicted model.
      </td>