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Exploration of Sugar Compounds in the PDB Library

Identify 4 example groups of sugar compounds in the PDB, including macrolactones, polyketides, anthracycline relatives, lipopolysaccharides, and blood group antigens. Search for natural metabolite sources and common names.

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Exploration of Sugar Compounds in the PDB Library

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  1. Assignment for next lecture Today has been a general view of sugars in the PDB For next week - Find all instances of the following 4 example groups of sugar compounds Caution: The compounds may be given as a single 3-letter code or as a LINKed set of chem_comp’s Find common name and if a natural metabolite what is the organism source EXCLUDE all phosphate and nucleotide examples

  2. Group 1 Sugar(s) attached to ring system (from 10 to 20 membered ring) Macrolactone, Polyketide - Antibiotics Not all ring systems with sugars attached are Macrolydes

  3. Group 2 Glycosylated relatives of anthracycline family that is given as a treatment for some types of cancer e.g. Daunomycin

  4. Group 3 Any thing that looks vaguely like a Lipopolysaccharide Clue look at pdb 1qff

  5. Group 4 Look for textual searching for anything that could be a Blood Group Antigen NOTE: Usually linked mono-saccharides so no COMPND/MOLECULE name [BUT not always e.g. look at DR3] and TITLE may be misleading as for a related series of PDB entries may be replicated to say complex with a blood group even for apo structures THE LEWIS B HUMAN BLOOD GROUP DETERMINANT

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