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Glycosciences.DB structure entry #8067: 3'-Sialyl T antigen (alpha-anomeric form)

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Format: CarbBank LINUCS GlycoCT_condensed GlycoCT_xml


 a-D-Neup5Ac-(2-3)-b-D-Galp-(1-3)-a-D-GalpNAc


RES
1b:a-dgal-HEX-1:5
2s:n-acetyl
3b:b-dgal-HEX-1:5
4b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d
5s:n-acetyl
LIN
1:1d(2+1)2n
2:1o(3+1)3d
3:3o(3+2)4d
4:4d(5+1)5n


<?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>
 <basetype id="4" anomer="a" superclass="non" ringStart="2" ringEnd="6" name="a-dgro-dgal-NON-2:6|1:a|2:keto|3:d">
 <stemtype id="1" type="dgro" />
 <stemtype id="2" type="dgal" />
 <modification type="a" pos_one="1" />
 <modification type="keto" pos_one="2" />
 <modification type="d" pos_one="3" />
 </basetype>
 <substituent id="5" name="n-acetyl" />
 </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>
 <connection id="3" parent="3" child="4">
 <linkage id="3" parentType="o" childType="d">
 <parent pos="3" />
 <child pos="2" />
 </linkage>
 </connection>
 <connection id="4" parent="4" child="5">
 <linkage id="4" parentType="d" childType="n">
 <parent pos="5" />
 <child pos="1" />
 </linkage>
 </connection>
 </linkages>
 </sugar>

SNFG-style Graphics

3D Structure Model

download coordinates

Corresponding entries: 12

1 - 5 of 12 entries with matching glycan part

Structure entry #525:

a-D-Neup5Ac-(2-3)-b-D-Galp-(1-3)-a-D-GalpNAc-(1-1)-Ethyl

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #526:

a-D-Neup5Ac-(2-3)-b-D-Galp-(1-3)-a-D-GalpNAc-(1-1)-<Ethylbromide>

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #2181:

a-D-Neup5Ac-(2-3/6)-b-D-Galp-(1-3)-a-D-GalpNAc

no NMR spectra

literature references

no GlycoMaps

Structure entry #3161: 3'-Sialyl T antigen linked to Ser

a-D-Neup5Ac-(2-3)-b-D-Galp-(1-3)-a-D-GalpNAc-(1-3)-Ser

NMR spectra

literature references

no GlycoMaps

Structure entry #4307: 3'-Sialyl T antigen linked to Thr

a-D-Neup5Ac-(2-3)-b-D-Galp-(1-3)-a-D-GalpNAc-(1-3)-Thr

no NMR spectra

literature references

no GlycoMaps

O-glycan core1 (Show) (Search Database)

3'Sialyl T antigen
Sialyl T antigen
sTa

General Structure Data

Chemical Formula:	C₂₅H₄₂N₂O₁₉		#C	#H	#O	#N
Molec. Weight:	674		25	42	19	2
# Atoms:	88
# Residues:	3
# Heavy Atoms:	46

Superclasses:

Neu		Hex
NeuAc	1	Hex	1
		HexNAc	1

Residues:

Residue	Count
A-D-GALPNAC	1
A-D-NEUP5AC	1
B-D-GALP	1

PDB references: 4

1 - 4 of 4 PDB entries

PDB ID 6efd: Hsa Siglec and Unique domains in complex with the sialyl T antigen trisaccharide

Description:

Source: Streptococcus gordonii str. Challis

Experimental method: X-RAY DIFFRACTION

Resolution: 1.85Å

Release date: 2020-02-19

Entry features 1 distinct glycan structures [1 instances].

PDB ID 5ij3: SrpA adhesin in complex with sialyl T antigen

Description: Platelet-binding glycoprotein

Source: Streptococcus sanguinis (strain SK36)

Experimental method: X-RAY DIFFRACTION

Resolution: 1.7Å

Release date: 2017-02-08

Entry features 1 distinct glycan structures [1 instances].

PDB ID 5iuc: Crystal structure of the GspB siglec domain with sialyl T antigen bound

Description: Platelet binding protein GspB

Source: Streptococcus gordonii

Experimental method: X-RAY DIFFRACTION

Resolution: 1.253Å

Release date: 2016-04-13

Entry features 1 distinct glycan structures [2 instances].

Description:

Source:

Experimental method: X-ray Diffraction

Resolution: 1.52Å

Release date:

Entry features 1 distinct glycan structures [4 instances].

Literature references: 8

1 - 5 of 8 literature references

Reference #21986

Zhang J; Zhang Z; Holst S; Blöchl C; Madunic K; Wuhrer M; Ten Dijke P; Zhang T

Transforming growth factor-β challenge alters the N-, O-, and glycosphingolipid glycomes in PaTu-S pancreatic adenocarcinoma cells.

Published 2022 in J Biol Chem, 298: 101717

Reference contains 26 structures

Reference #21813

White B; Patterson M; Karnwal S; Brooks CL

Crystal structure of a human MUC16 SEA domain reveals insight into the nature of the CA125 tumor marker.

Published 2022 in Proteins, : epub ahead of print

Reference contains 11 structures

Reference #20891

Cancer glycan epitopes: biosynthesis, structure and function.

Published 2018 in Glycobiology, 28: 670-696

Reference contains 26 structures

Reference #20556

Bensing BA; Khedri Z; Deng L; Yu H; Prakobphol A; Fisher SJ; Chen X; Iverson TM; Varki A; Sullam PM

Novel aspects of sialoglycan recognition by the Siglec-like domains of streptococcal SRR glycoproteins.

Published 2016 in Glycobiology, 26: 1222-1234

Reference contains 11 structures

Reference #21045

Joncquel Chevalier Curt M; Lecointe K; Mihalache A; Rossez Y; Gosset P; Léonard R; Robbe-Masselot C

Alteration or adaptation, the two roads for human gastric mucin glycosylation infected by Helicobacter pylori.

Published 2015 in Glycobiology, 25: 617-31

Reference contains 51 structures

Further literature references from PDB entries: 3

1 - 3 of 3 literature references from PDB entries

Reference #22086

Bensing BA; Stubbs HE; Agarwal R; Yamakawa I; Luong K; Solakyildirim K; Yu H; Hadadianpour A; Castro MA; Fialkowski KP; Morrison KM; Wawrzak Z; Chen X; Lebrilla CB; Baudry J; Smith JC; Sullam PM; Iverson TM

Origins of glycan selectivity in streptococcal Siglec-like adhesins suggest mechanisms of receptor adaptation.

Published 2022 in Nat Commun, 13: 2753

Reference #20156

Loukachevitch LV; Bensing BA; Yu H; Zeng J; Chen X; Sullam PM; Iverson TM

Structures of the Streptococcus sanguinis SrpA Binding Region with Human Sialoglycans Suggest Features of the Physiological Ligand.

Published 2016 in Biochemistry, :

Reference #17908

Pyburn TM; Bensing BA; Xiong YQ; Melancon BJ; Tomasiak TM; Ward NJ; Yankovskaya V; Oliver KM; Cecchini G; Sulikowski GA; Tyska MJ; Sullam PM; Iverson TM

A structural model for binding of the serine-rich repeat adhesin GspB to host carbohydrate receptors.

Published 2011 in PLoS Pathog., 7: e1002112

Consortium for Functional Glycomics (CFG):

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