Protein crosslinks: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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 ====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". Adding "and not thioesterase" reduced the hits to ~500. 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 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.
-**Example: Bacterial pilus adhesin [[2xi9]] has 2 thioester bonds (and 2 isopeptide bonds).
+*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".
-**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.
+*Adding "and not thioesterase" to the PDBe search reduced the hits to ~500.
+*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.
 ==Artificial Crosslinks==