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Glycosciences.DB structure entry #149: 3'-Sialyl-LewisX tetrasaccharide (beta-anomeric form)

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Format: CarbBank LINUCS GlycoCT_condensed GlycoCT_xml


 a-D-Neup5Ac-(2-3)-b-D-Galp-(1-4)+
                                 |
                            b-D-GlcpNAc
                                 |
                   a-L-Fucp-(1-3)+


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


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

SNFG-style Graphics

3D Structure Model

download coordinates

Corresponding entries: 13

1 - 5 of 13 entries with matching glycan part

Structure entry #1713:

a-D-Neup5Ac-(2-3)-b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-5)-5-hydroxy-hexanoate-(1-1)-Methyl | a-L-Fucp-(1-3)+

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #2173: 3'-Sialyl Lewis X antigen, CD15s

a-D-Neup5Ac-(2-3)-b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-3)-<rest of molecule> | a-L-Fucp-(1-3)+

no 3d model

no NMR spectra

literature references

no GlycoMaps

Structure entry #2218:

a-D-Neup5Ac-(2-3)-b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-1)-Allyl | a-L-Fucp-(1-3)+

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #2293:

a-D-Neup5Ac-(2-3)-b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-4)-Asn-(1-2)-Gly-(1-2)-Phe | a-L-Fucp-(1-3)+

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #4519:

a-D-Neup5Ac-(2-3)-b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-1)-ethanolamine | a-L-Fucp-(1-3)+

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Sialyl Lewis X (Show) (Search Database)

SSEA-1
SSEA1
stage-specific embryonic antigen 1
sLeX
Sialyl Lewis X
3'sLex
Sia-LeX
3'Sia-LeX

General Structure Data

Chemical Formula:	C₃₁H₅₂N₂O₂₃		#C	#H	#O	#N
Molec. Weight:	820		31	52	23	2
# Atoms:	108
# Residues:	4
# Heavy Atoms:	56

Superclasses:

Neu		Hex
NeuAc	1	Hex	1
		dHex	1
		HexNAc	1

Residues:

Residue	Count
A-D-NEUP5AC	1
A-L-FUCP	1
B-D-GALP	1
B-D-GLCPNAC	1

PDB references: 8

1 - 5 of 8 PDB entries

PDB ID 5kiq: SrpA with sialyl LewisX

Description: Platelet-binding glycoprotein

Source: Streptococcus sanguinis (strain SK36)

Experimental method: X-RAY DIFFRACTION

Resolution: 1.638Å

Release date: 2017-05-24

Entry features 1 distinct glycan structures [1 instances].

PDB ID 4uso: X-ray structure of the CCL2 lectin in complex with sialyl lewis X

Description: CCL2 LECTIN

Source: COPRINOPSIS CINEREA

Experimental method: X-RAY DIFFRACTION

Resolution: 1.95Å

Release date: 2015-07-22

Entry features 1 distinct glycan structures [1 instances].

PDB ID 4rfb: 1.93 Angstrom Crystal Structure of Superantigen-like Protein from Staphylococcus aureus in Complex with Sialyl-Lewis X.

Description: Putative uncharacterized protein

Source: Staphylococcus aureus subsp. aureus

Experimental method: X-RAY DIFFRACTION

Resolution: 1.93Å

Release date: 2014-10-08

Entry features 1 distinct glycan structures [4 instances].

PDB ID 4uo2: Structure of the A_Equine_Richmond_07 H3 haemagglutinin in complex with Sialyl Lewis X

Description: H3 HAEMAGGLUTININ HA1 CHAIN, H3 HAEMAGGLUTININ HA2 CHAIN

Source:

Experimental method: X-RAY DIFFRACTION

Resolution: 2.7Å

Release date: 2014-07-23

Entry features 10 distinct glycan structures [25 instances].

PDB ID 2r61: Crystal structure of the Staphylococcal superantigen-like protein SSL5 in complex with sialyl-Lewis X at pH 7.4

Description: Exotoxin 3

Source: Staphylococcus aureus

Experimental method: X-RAY DIFFRACTION

Resolution: 2.75Å

Release date: 2007-11-27

Entry features 1 distinct glycan structures [1 instances].

Literature references: 230

1 - 5 of 230 literature references

Reference #21785

Walker MR; Goel HL; Mukhopadhyay D; Chhoy P; Karner ER; Clark JL; Liu H; Li R; Zhu JL; Chen S; Mahal LK; Bensing BA; Mercurio AM

O-linked α2,3 sialylation defines stem cell populations in breast cancer.

Published 2022 in Sci Adv, 8: eabj9513

Reference contains 5 structures

Reference #21646

Šmak P; Chandrabose S; Tvaroška I; Koča J

Pan-selectin inhibitors as potential therapeutics for COVID-19 treatment: in silico screening study.

Published 2021 in Glycobiology, 31: 975-987

Reference contains 1 structure

Reference #21703

Ezeabikwa B; Mondal N; Antonopoulos A; Haslam SM; Matsumoto Y; Martin-Caraballo M; Lehoux S; Mandalasi M; Ishaque A; Heimburg-Molinaro J; Cummings RD; Nyame AK

Major differences in glycosylation and fucosyltransferase expression in low-grade versus high-grade bladder cancer cell lines.

Published 2021 in Glycobiology, 31: 1444-1463

Reference contains 15 structures

Reference #22000

Sojitra M; Sarkar S; Maghera J; Rodrigues E; Carpenter EJ; Seth S; Ferrer Vinals D; Bennett NJ; Reddy R; Khalil A; Xue X; Bell MR; Zheng RB; Zhang P; Nycholat C; Bailey JJ; Ling CC; Lowary TL; Paulson JC; Macauley MS; Derda R

Genetically encoded multivalent liquid glycan array displayed on M13 bacteriophage.

Published 2021 in Nat Chem Biol, 17: 806-816

Reference contains 65 structures

Reference #21602

Hyun JY; Kim S; Lee CH; Lee HS; Shin I

Efficient Preparation and Bioactivity Evaluation of Glycan-Defined Glycoproteins.

Published 2021 in ACS Chem Biol, 16: 1930-1940

Reference contains 9 structures

Further literature references from PDB entries: 3

1 - 3 of 3 literature references from PDB entries

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 #16968

Baker HM; Basu I; Chung MC; Caradoc-Davies T; Fraser JD; Baker EN

Crystal structures of the staphylococcal toxin SSL5 in complex with sialyl Lewis X reveal a conserved binding site that shares common features with viral and bacterial sialic acid binding proteins.

Published 2007 in J. Mol. Biol., 374: 1298-308

Reference #19806

Structure of a selectin-like mutant of mannose-binding protein complexed with sialylated and sulfated Lewis(x) oligosaccharides.

Published 1997 in Biochemistry, 36: 979-88

NCBI Taxonomy ID	Scientific Name
10029	Cricetulus griseus
9031	Gallus gallus
9606	Homo sapiens
9544	Macaca mulatta
10090	Mus musculus

Consortium for Functional Glycomics (CFG):

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