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Glycosciences.DB structure entry #672: Thomsen-Friedenreich (TF) antigen / Mucin-type O-glycan core 1 (Ser-linked)

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Format: CarbBank LINUCS GlycoCT_xml


 b-D-Galp-(1-3)-a-D-GalpNAc-(1-3)-Ser


<?xml version="1.0" encoding="UTF-8"?>
 <sugar version="1.0">
 <residues>
 <basetype id="1" anomer="a" superclass="hex" ringStart="1" ringEnd="5" name="a-dgal-HEX-1:5">
 <stemtype id="1" type="dgal" />
 </basetype>
 <substituent id="2" name="n-acetyl" />
 <basetype id="3" anomer="b" superclass="hex" ringStart="1" ringEnd="5" name="b-dgal-HEX-1:5">
 <stemtype id="1" type="dgal" />
 </basetype>
 </residues>
 <linkages>
 <connection id="1" parent="1" child="2">
 <linkage id="1" parentType="d" childType="n">
 <parent pos="2" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="2" parent="1" child="3">
 <linkage id="2" parentType="o" childType="d">
 <parent pos="3" />
 <child pos="1" />
 </linkage>
 </connection>
 </linkages>
 <aglyca>
 <historicalData>
 <entry id="0" name="SER" toResidue="1">
 <linkage parentType="n" childType="x">
 <parent pos="3" />
 <child pos="1" />
 </linkage>
 </entry>
 </historicalData>
 </aglyca>
 </sugar>

SNFG-style Graphics

3D Structure Model

download coordinates

Corresponding entries: 44

1 - 5 of 44 entries with matching glycan part

Structure entry #571:

b-D-Galp-(1-3)-a-D-GalpNAc-(1-3)+ | b-D-Galp-(1-3)-a-D-GalpNAc-(1-3)+ Ser | | Ser-(1-2)+ | b-D-Galp-(1-3)-a-D-GalpNAc-(1-3)-Ser-(1-2)+

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #578:

b-D-Galp-(1-3)-a-D-GalpNAc-(1-3)+ | Thr-(1-2)-Ser-(1-2)-Ser | Ala-(1-2)-Pro-(1-2)+

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #584: SST peptide with two T antigens

b-D-Galp-(1-3)-a-D-GalpNAc-(1-3)+ | b-D-Galp-(1-3)-a-D-GalpNAc-(1-3)+ Thr | | Ser-(1-2)+ | Ser-(1-2)+

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #611: Thomsen-Friedenreich (TF) antigen (glycan part)

b-D-Galp-(1-3)-a-D-GalpNAc

NMR spectra

literature references

GlycoMaps

Structure entry #2332:

b-D-Galp-(1-3)-a-D-GalpNAc-(1-1)-<Crotyl-KLH/HSA>

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

O-glycan core1 (Show) (Search Database)

Thomsen-Friedenreich antigen
TF antigen
T antigen

Thomsen-Friedenreich antigen
TF antigen
T antigen

General Structure Data

Chemical Formula:	C₁₇H₃₀N₂O₁₂		#C	#H	#O	#N
Molec. Weight:	454		17	30	12	2
# Atoms:	61
# Residues:	3
# Heavy Atoms:	31

Superclasses:

Hex
Hex	1
HexNAc	1

Residues:

Residue	Count
A-D-GALPNAC	1
B-D-GALP	1
SER	1

PDB references: 7

1 - 5 of 7 PDB entries

PDB ID 7jtv: Structure of IMPa from Pseudomonas aeruginosa in complex with an O-glycopeptide

Description: Immunomodulating metalloprotease (E.C.3.4.24.-), GLU-ALA-PRO-SER-ALA

Source: Pseudomonas aeruginosa

Experimental method: X-RAY DIFFRACTION

Resolution: 2.45Å

Release date: 2020-12-16

Entry features 1 distinct glycan structures [2 instances].

PDB ID 5kdx: IMPa metallopeptidase in complex with T-antigen

Description: Metallopeptidase

Source:

Experimental method: X-RAY DIFFRACTION

Resolution: 2.4Å

Release date: 2017-01-11

Entry features 1 distinct glycan structures [2 instances].

PDB ID 5a58: The structure of GH101 D764N mutant from Streptococcus pneumoniae TIGR4 in complex with serinyl T-antigen

Description: ENDO-ALPHA-GALACTOSAMINIDASE

Source: STREPTOCOCCUS PNEUMONIAE

Experimental method: X-RAY DIFFRACTION

Resolution: 1.8Å

Release date: 2015-09-02

Entry features 1 distinct glycan structures [1 instances].

PDB ID 4i4y: BEL beta-trefoil complex with T-Antigen

Description: BEL beta-trefoil

Source: Boletus edulis

Experimental method: X-RAY DIFFRACTION

Resolution: 1.9Å

Release date: 2013-04-24

Entry features 1 distinct glycan structures [6 instances].

PDB ID 1y2v: Crystal structure of the common edible mushroom (Agaricus bisporus) lectin in complex with T-antigen

Description: lectin

Source: Agaricus bisporus

Experimental method: X-RAY DIFFRACTION

Resolution: 1.9Å

Release date: 2004-12-21

Entry features 1 distinct glycan structures [2 instances].

Literature references: 75

1 - 5 of 75 literature references

Reference #21993

Konstantinidi A; Nason R; Čaval T; Sun L; Sørensen DM; Furukawa S; Ye Z; Vincentelli R; Narimatsu Y; Vakhrushev SY; Clausen H

Exploring the glycosylation of mucins by use of O-glycodomain reporters recombinantly expressed in glycoengineered HEK293 cells.

Published 2022 in J Biol Chem, 298: 101784

Reference contains 10 structures

Reference #21956

Sim L; Thompson N; Geissner A; Withers SG; Wakarchuk WW

Mammalian sialyltransferases allow efficient Escherichia coli-based production of mucin-type O-glycoproteins but can also transfer Kdo.

Published 2022 in Glycobiology, 32: 429-440

Reference contains 12 structures

Reference #21599

Wardman JF; Rahfeld P; Liu F; Morgan-Lang C; Sim L; Hallam SJ; Withers SG

Discovery and Development of Promiscuous O-Glycan Hydrolases for Removal of Intact Sialyl T-Antigen.

Published 2021 in ACS Chem Biol, 16: 2004-2015

Reference contains 8 structures

Reference #21629

Stewart TJ; Takahashi K; Xu N; Prakash A; Brown R; Raska M; Renfrow MB; Novak J

Quantitative assessment of successive carbohydrate additions to the clustered O-glycosylation sites of IgA1 by glycosyltransferases.

Published 2021 in Glycobiology, 31: 540-556

Reference contains 12 structures

Reference #21698

Zeng J; Aryal RP; Stavenhagen K; Luo C; Liu R; Wang X; Chen J; Li H; Matsumoto Y; Wang Y; Wang J; Ju T; Cummings RD

Cosmc deficiency causes spontaneous autoimmunity by breaking B cell tolerance.

Published 2021 in Sci Adv, 7: eabg9118

Reference contains 2 structures

Further literature references from PDB entries: 3

1 - 3 of 3 literature references from PDB entries

Reference #19304

Gregg KJ; Suits MD; Deng L; Vocadlo DJ; Boraston AB

Structural Analysis of a Family 101 Glycoside Hydrolase in Complex with Carbohydrates Reveals Insights into Its Mechanism.

Published 2015 in J. Biol. Chem., 290: 25657-69

Reference #18366

Bovi M; Cenci L; Perduca M; Capaldi S; Carrizo ME; Civiero L; Chiarelli LR; Galliano M; Monaco HL

BEL β-trefoil: a novel lectin with antineoplastic properties in king bolete (Boletus edulis) mushrooms.

Published 2013 in Glycobiology, 23: 578-92

Reference #16423

Carrizo ME; Irazoqui FJ; Lardone RD; Nores GA; Curtino JA; Capaldi S; Perduca M; Monaco HL

Crystallization and preliminary X-ray study of the common edible mushroom (Agaricus bisporus) lectin.

Published 2004 in Acta Crystallogr. D Biol. Crystallogr., 60: 718-20

NCBI Taxonomy ID	Scientific Name
10029	Cricetulus griseus
9606	Homo sapiens
10090	Mus musculus
9986	Oryctolagus cuniculus

Consortium for Functional Glycomics (CFG):

GlycoEpitope DB:

EP0020

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