Ya-Min Chi
Sarah Goodman
Sugars
DNA
Others
RNA
Nucleic Acid
Containing
Mixed
OGlycan
Carbohydrates
Glycoproteins
NGlycan
CGlycan
P-Glycan
All Entries
NonCarbohydrates
Proteoglycans
GPI
Glycolipids
Glycerogl
ycolipid
Glycosphin
golipids
Heparin/Heparan
Sulfate
Chondroition
Sulfate
Keratan
Sulfate
Hyaluroan
•
Sugars Bin- Any entry containing at least one
monosaccharide unit but not containing any protein, nucleic
acid, and lipids.
Others Bin- Any entry containing at least one
monosaccharide unit that interacts with protein non-covalently.
Nucleic Acid Containing Bin- Any entry containing at least
one monosaccharide unit that also contain nucleic acid.
Glycoproteins Bin- proteins that contain oligosaccharide
chains (glycans) covalently attached to polypeptide sidechains. N-glycosylation and O-glycosylation with
comparatively small, branched, usually unsulfated
carbohydrate units, devoid of repeating units.
•
Proteoglycans Bin- proteins that are heavily glycosylated.
The basic proteoglycan unit consists of a "core protein" with
one or more covalently attached glycosaminoglycan (GAG)
chain(s). Ser-linked and consist of long, unbranched chains of
alternating residues of hexosamine and uronic acid or
galactose
Glycolipids Bin- any entry that contains both carbohydrate
and lipid moieties. The term glycolipid designates any
compound containing one or more monosaccharide residues
bound by a glycosidic linkage to a hydrophobic moiety such as
an acylglycerol, a sphingoid, a ceramide (N-acylsphingoid) or
a prenyl phosphate.
•
•
20 entries (15 entries are GAGs)
Of the 15 entries
– submitted by 4 groups.
– 1 classified as GAGs, 5 as carbohydrates, 8 as
texture of connective tissue, and 1 as cell adhesion.
•
Of the 5 entries
– By 3 groups
– 1 as carbohydrate, 1 as inhibitor, 2 as texture, and
1 as bacterial encapuslation.


Proteoglycans contain glycosaminoglycans,
which consist of repeating chains of certain
combinations of monosaccharides.
By doing a chemical component search for
each of these combinations, it should be
possible to find all glycosaminoglycans.
Chondroitin Keratan
Sulfate
Sulfate
GlcUAGalNAc
IdoUAGlcNAc
53
GalGlcNAc
145
Heparan
Sulfate
GlcUAGlcNAc
GlcUAGlcNS
IdoUAGlcNAc
IdoUAGlcNS
118
Hyaluronan
GlcUAGlcNAc
81

Glucuronic/ iduronic acid + N-Glucosamine
IDS
SGN
3DY0

Glucuronic/ iduronic acid + Galactosamine
1C4S

Galactose + N-Glucosamine
NGS
G6S
1KES

Glcuronic Acid + N-Glucosamine
BDP
NAG
2BVK
+
+
L42
UCD
H1S
H3S
H1SL42- Chondroitin
Heparan
Sulfate
Disaccharide
Overall, 9 PDB entries resulted from this
search.