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Progress in Classification Cont.

Progress in Classification Cont. Aileen Zaydel Sarah Goodman Ya-Min Chi. Sialic Acid. Sialic Acid contain ingentries- 224 Sialic Acid ligand- 33. Tasks for this week. Find all N-glycans and O-glycans Classify all remaining (~5000) entries Find all polysaccharides.

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Progress in Classification Cont.

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  1. Progress in Classification Cont. Aileen Zaydel Sarah Goodman Ya-Min Chi

  2. Sialic Acid Sialic Acid contain ingentries- 224 Sialic Acid ligand- 33

  3. Tasks for this week • Find all N-glycans and O-glycans • Classify all remaining (~5000) entries • Find all polysaccharides

  4. Finding Glycoproteins • Given the link records for all PDB entries that had SER, THR, or ASN in the link records. • Looked through these lists for O-glycans (SER and THR) and N-glycans (ASN).

  5. O-Glycan Results

  6. Problems/Questions- 1ZL0 SER TLA

  7. Problems/Questions- 1RWQ SER 87 NAG 794 NAG 794 ASN 85

  8. N-Glycan results Total Glycoproteins

  9. N-Glycan • 2372 Entries • There are some false positive • ASN and NAG are linked through N and O • Linked to other ligands besides NAG & NDG • GAD CBS HSQ MAN BGC 5AX G2F B6D BDP LXB GLC LXZ NGA

  10. Error in Linkage 1NFD

  11. False Positive

  12. C Glycan • Mannose linked to tryptophan • 3OJY (TRP BMA)

  13. Remainder • After we took out all N and O-glycans found in Shuchi’s generated list, we began sorting through the unclassified remainder Mono- and polysaccharides “Other”

  14. Mono and Polysaccharide Bin • Any entry that contains at least one monosacharide unit non-covalently bound to the protein. Monosaccharides can be covalently bound to each other, forming a polysaccharide. • Subclassified into modified and unmodified saccharides. Modifications are annotated.

  15. 3P5D MAN

  16. “Other” Bin • Any entry that contains at least one monosaccharide unit non-covalently attached to protein but covalently attached to unique structures that are not lipids, sugars, amino acids, etc. • Includes antibiotics

  17. 1D0M Antibiotic Buglecin A

  18. We also found… • Straight chain sugars and acids • Sugars linked to amino acids other than ASN, SER, THR • GLU, ALA, ASP

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