Protein crosslinks: Difference between revisions

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Eric Martz

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 [[Disulfide bonds]] are the most common protein crosslinks. About 23% of protein structures in the [[PDB]] have disulfide bonds (July, 2021<ref>In July, 2021, the PDB had ~180,000 entries. Advanced search at RCSB.Org for "Polymer molecuar features: polymer entity type = protein" and "Deposited entry features: Disulfide bond count per deposited model > 0" gave ~41,000 hits, or about 23%.</ref>).
 *Example: Insulin [[9ins]] has 2 interchain and one intrachain disulfide bonds.
 *Visualization: [https://firstglance.jmol.org/fg.htm?mol=9ins View 9ins in FirstGlance]. In [[FirstGlance]], in the Tools Tab, click Disulfides/S/Se.
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 [[Isopeptide bonds]] are less common, but an estimate of their frequency may not be available. A text search for "isopeptide" at RCSB.Org gives ~400 hits, while a text search at PDBe gives ~12,000 hits (July, 2021). In a small sample of the latter hits, none contained the term "isopeptide". Also based on a small sample, some entries that contain verified isopeptide bonds do not contain the term.
 *Example: Bacterial pilus adhesin [[2xi9]] has 2 isopeptide bonds (and 2 thioester bonds).
 *Visualization: [https://firstglance.jmol.org/fg.htm?mol=2xi9 View 2xi9 in FirstGlance]. If you see "<span style='color:#00d0a0;'>&#10148;&#10148;</span><u>Show more details</u>" in the [http://firstglance.jmol.org/where.htm#mit Molecule Information Tab], click on that.
-*<big>[[Thioester protein crosslinks|Thioester bonds]]</big>: Again, an estimate of frequency may not be available. A text search for "thioester" at RCSB.Org gives ~2,000 hits, while a text search at PDBe gives ~1,400 hits (July, 2021). Among a sample of 5 of the PDBe hits (every 100th in the listing), none had thioester bonds, but most contained terms such as "thioesterase" or "thioester". RCSB Advanced Search has "Biologically Interesting Molecules (BIRD): BIRD Type = Thioester", which gives 19 hits (July, 2021). However, only 2% of entries have BIRD annotations.
+====Thioester Bonds====
-**Example: Bacterial pilus adhesin [[2xi9]] has 2 isopeptide bonds (and 2 thioester bonds).
+[[Thioester protein crosslinks|Thioester bonds]]: Again, an estimate of frequency may not be available. A text search for "thioester" at RCSB.Org gives ~2,000 hits, while a text search at PDBe gives ~1,400 hits (July, 2021). Among a sample of 5 of the PDBe hits (every 100th in the listing), none had thioester bonds, but most contained terms such as "thioesterase" or "thioester". RCSB Advanced Search has "Biologically Interesting Molecules (BIRD): BIRD Type = Thioester", which gives 19 hits (July, 2021). However, only 2% of entries have BIRD annotations.
+**Example: Bacterial pilus adhesin [[2xi9]] has 2 thioester bonds (and 2 isopeptide bonds).
 **Visualization: [https://firstglance.jmol.org/fg.htm?mol=2xi9 View 2xi9 in FirstGlance]. If you see "<span style='color:#00d0a0;'>&#10148;&#10148;</span><u>Show more details</u>" in the [http://firstglance.jmol.org/where.htm#mit Molecule Information Tab], click on that.