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Glycosciences.DB structure entry #22742: LS-Tetrasaccharide c / LST c

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Format: CarbBank LINUCS GlycoCT_condensed GlycoCT_xml


a-D-Neup5Ac-(2-6)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-Glcp


RES
1b:b-dglc-HEX-1:5
2b:b-dgal-HEX-1:5
3b:b-dglc-HEX-1:5
4s:n-acetyl
5b:b-dgal-HEX-1:5
6b:a-dgro-dgal-NON-2:6|1:a|2:keto|3:d
7s:n-acetyl
LIN
1:1o(4+1)2d
2:2o(3+1)3d
3:3d(2+1)4n
4:3o(4+1)5d
5:5o(6+2)6d
6:6d(5+1)7n


<?xml version="1.0" encoding="UTF-8"?>
 <sugar version="1.0">
 <residues>
 <basetype id="1" anomer="b" superclass="hex" ringStart="1" ringEnd="5" name="b-dglc-HEX-1:5">
 <stemtype id="1" type="dglc" />
 </basetype>
 <basetype id="2" anomer="b" superclass="hex" ringStart="1" ringEnd="5" name="b-dgal-HEX-1:5">
 <stemtype id="1" type="dgal" />
 </basetype>
 <basetype id="3" anomer="b" superclass="hex" ringStart="1" ringEnd="5" name="b-dglc-HEX-1:5">
 <stemtype id="1" type="dglc" />
 </basetype>
 <substituent id="4" name="n-acetyl" />
 <basetype id="5" anomer="b" superclass="hex" ringStart="1" ringEnd="5" name="b-dgal-HEX-1:5">
 <stemtype id="1" type="dgal" />
 </basetype>
 <basetype id="6" 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="7" name="n-acetyl" />
 </residues>
 <linkages>
 <connection id="1" parent="1" child="2">
 <linkage id="1" parentType="o" childType="d">
 <parent pos="4" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="2" parent="2" 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="d" childType="n">
 <parent pos="2" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="4" parent="3" child="5">
 <linkage id="4" parentType="o" childType="d">
 <parent pos="4" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="5" parent="5" child="6">
 <linkage id="5" parentType="o" childType="d">
 <parent pos="6" />
 <child pos="2" />
 </linkage>
 </connection>
 <connection id="6" parent="6" child="7">
 <linkage id="6" parentType="d" childType="n">
 <parent pos="5" />
 <child pos="1" />
 </linkage>
 </connection>
 </linkages>
 </sugar>

SNFG-style Graphics

3D Structure Model

download coordinates

Corresponding entries: 1

1 - 1 of 1 entries with matching glycan part

Structure entry #748:

a-D-Neup5Ac-(2-6)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-b-D-Galp-(1-4)-b-D-Glcp-(1-1)-Ceramide

no 3d model

no NMR spectra

literature references

no GlycoMaps

GSL core, neolacto-type (Show) (Search Database)

LSTc
LST c
LS-Tetrasaccharide c

Superclasses:

Neu		Hex
NeuAc	1	Hex	3
		HexNAc	1

Residues:

Residue	Count
A-D-NEUP5AC	1
B-D-GALP	2
B-D-GLCP	1
B-D-GLCPNAC	1

PDB references: 7

1 - 5 of 7 PDB entries

PDB ID 5xrs: Crystal structure of A/Minnesota/11/2010 (H3N2) influenza virus hemagglutinin in complex with LSTc

Description: Hemagglutinin

Source: Influenza A virus (A/swine/Minnesota/A01134337/2010(H3N2))

Experimental method: X-RAY DIFFRACTION

Resolution: 2.907Å

Release date: 2018-07-25

Entry features 12 distinct glycan structures [32 instances].

PDB ID 4x13: JC Polyomavirus genotype 3 VP1 in complex with LSTc pentasaccharide

Description: JC polyomavirus VP1 from a genotype 3 strain

Source: JC polyomavirus type 3

Experimental method: X-RAY DIFFRACTION

Resolution: 2Å

Release date: 2015-04-22

Entry features 2 distinct glycan structures [3 instances].

PDB ID 2yp4: Haemagglutinin of 2004 Human H3N2 Virus in Complex with Human Receptor Analogue LSTc

Description: HEMAGGLUTININ

Source: INFLUENZA A VIRUS

Experimental method: X-RAY DIFFRACTION

Resolution: 1.85Å

Release date: 2012-11-07

Entry features 4 distinct glycan structures [7 instances].

PDB ID 2ypg: Haemagglutinin of 1968 Human H3N2 Virus in Complex with Human Receptor Analogue LSTc

Description: HEMAGGLUTININ HA1 CHAIN, HEMAGGLUTININ HA2 CHAIN

Source: Influenza A virus (A/X-31(H3N2))

Experimental method: X-RAY DIFFRACTION

Resolution: 2.85Å

Release date: 2012-11-07

Entry features 7 distinct glycan structures [17 instances].

PDB ID 3nxd: JC polyomavirus VP1 in complex with LSTc

Description: Major capsid protein VP1

Source: JC polyomavirus

Experimental method: X-RAY DIFFRACTION

Resolution: 2Å

Release date: 2010-11-17

Entry features 1 distinct glycan structures [2 instances].

Literature references: 7

1 - 5 of 7 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 #22508

Munday RJ; Coradin T; Nimmo R; Lad Y; Hyde SC; Mitrophanos K; Gill DR

Sendai F/HN pseudotyped lentiviral vector transduces human ciliated and non-ciliated airway cells using α 2,3 sialylated receptors.

Published 2022 in Mol Ther Methods Clin Dev, 26: 239-252

Reference contains 7 structures

Reference #21814

Roderer D; Bröcker F; Sitsel O; Kaplonek P; Leidreiter F; Seeberger PH; Raunser S

Glycan-dependent cell adhesion mechanism of Tc toxins.

Published 2020 in Nat Commun, 11: 2694

Reference contains 13 structures

Reference #20425

Macchi E; Rudd TR; Raman R; Sasisekharan R; Yates EA; Naggi A; Guerrini M; Elli S

Nuclear Magnetic Resonance and Molecular Dynamics Simulation of the Interaction between Recognition Protein H7 of the Novel Influenza Virus H7N9 and Glycan Cell Surface Receptors.

Published 2016 in Biochemistry, 55: 6605-6616

Reference contains 2 structures

Reference #19169

Ströh LJ; Maginnis MS; Blaum BS; Nelson CD; Neu U; Gee GV; O'Hara BA; Motamedi N; DiMaio D; Atwood WJ; Stehle T

The Greater Affinity of JC Polyomavirus Capsid for α2,6-Linked Lactoseries Tetrasaccharide c than for Other Sialylated Glycans Is a Major Determinant of Infectivity.

Published 2015 in J. Virol., 89: 6364-75

Reference contains 5 structures

Further literature references from PDB entries: 4

1 - 4 of 4 literature references from PDB entries

Reference #20561

Bangaru S; Zhang H; Gilchuk IM; Voss TG; Irving RP; Gilchuk P; Matta P; Zhu X; Lang S; Nieusma T; Richt JA; Albrecht RA; Vanderven HA; Bombardi R; Kent SJ; Ward AB; Wilson IA; Crowe JE

A multifunctional human monoclonal neutralizing antibody that targets a unique conserved epitope on influenza HA.

Published 2018 in Nat Commun, 9: 2669

Reference #18379

Lin YP; Xiong X; Wharton SA; Martin SR; Coombs PJ; Vachieri SG; Christodoulou E; Walker PA; Liu J; Skehel JJ; Gamblin SJ; Hay AJ; Daniels RS; McCauley JW

Evolution of the receptor binding properties of the influenza A(H3N2) hemagglutinin.

Published 2012 in Proc. Natl. Acad. Sci. U.S.A., 109: 21474-9

Reference #16388

Gamblin SJ; Haire LF; Russell RJ; Stevens DJ; Xiao B; Ha Y; Vasisht N; Steinhauer DA; Daniels RS; Elliot A; Wiley DC; Skehel JJ

The structure and receptor binding properties of the 1918 influenza hemagglutinin.

Published 2004 in Science, 303: 1838-42

Reference #15985

Ha Y; Stevens DJ; Skehel JJ; Wiley DC

X-ray structures of H5 avian and H9 swine influenza virus hemagglutinins bound to avian and human receptor analogs.

Published 2001 in Proc. Natl. Acad. Sci. U.S.A., 98: 11181-6

Consortium for Functional Glycomics (CFG):

carbNlink_45541_D000

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