Chains and Chain IDs: Difference between revisions
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===Oligosaccharide Chain IDs=== | ===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=== | ===Chain ID Assignment Policies=== | ||
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===AlphaFold3 Chain IDs=== | ===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 [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"> | <table class="wikitable"> | ||
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<td> | <td> | ||
1 ID total: | 1 ID total: | ||
:Protein,Zn++,Monomeric mannose glycoconjugates: A | :Protein, Zn++, Monomeric mannose glycoconjugates: <b>A</b>. | ||
</td> | </td> | ||
<td> | <td> | ||
8 IDs total: | 8 IDs total: | ||
<br> | <br> | ||
:Protein: A. | :Protein: <b>A</b>. | ||
:1 Zn++: B. | :1 Zn++: <b>B</b>. | ||
:6 Monomeric mannose glycoconjugates: C,D,E,F,G,H. | :6 Monomeric mannose glycoconjugates: <b>C,D,E,F,G,H</b>. | ||
</td> | </td> | ||
<td> | <td> | ||
| Line 279: | Line 279: | ||
<td> | <td> | ||
3 IDs total: | 3 IDs total: | ||
:Protein,Ca++,Na+: A. | :Protein, Ca++, Na+: <b>A</b>. | ||
:DNA: B, C. | :DNA: <b>B, C</b>. | ||
</td> | </td> | ||
<td> | <td> | ||
7 IDs total: | 7 IDs total: | ||
<br> | <br> | ||
:Protein: A. | :Protein: <b>A</b>. | ||
:3 Ca++: B, C, D. | :3 Ca++: <b>B, C, D</b>. | ||
:1 Na+: E. | :1 Na+: <b>E</b>. | ||
:DNA: F, G. | :DNA: <b>F, G</b>. | ||
</td> | </td> | ||
<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> | </td> | ||
| Line 303: | Line 304: | ||
<td> | <td> | ||
3 IDs total: | 3 IDs total: | ||
:tRNA: 1. | :tRNA: <b>1</b>. | ||
:Protein + 1 Zn++: 2. | :Protein + 1 Zn++: <b>2</b>. | ||
:Protein + 1 Zn++: 3. | :Protein + 1 Zn++: <b>3</b>. | ||
</td> | </td> | ||
<td> | <td> | ||
5 IDs total: | 5 IDs total: | ||
<br> | <br> | ||
:Protein: A, B. | :Protein: <b>A, B</b>. | ||
:Zn++: C, D. | :Zn++: <b>C, D</b>. | ||
:tRNA: E. | :tRNA: <b>E</b>. | ||
</td> | </td> | ||
<td> | <td> | ||
