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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. 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
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).
Problems/Questions- 1ZL0 SER TLA
Problems/Questions- 1RWQ SER 87 NAG 794 NAG 794 ASN 85
N-Glycan results Total Glycoproteins
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
Error in Linkage 1NFD
C Glycan • Mannose linked to tryptophan • 3OJY (TRP BMA)
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”
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.
3P5D MAN
“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
1D0M Antibiotic Buglecin A
We also found… • Straight chain sugars and acids • Sugars linked to amino acids other than ASN, SER, THR • GLU, ALA, ASP