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Glycosciences.DB structure entry #1132: LewisY tetrasaccharide (beta-anomeric form)

Format: CarbBank LINUCS GlycoCT_condensed GlycoCT_xml


 a-L-Fucp-(1-2)-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-lgal-HEX-1:5|6:d
LIN
1:1d(2+1)2n
2:1o(3+1)3d
3:1o(4+1)4d
4:4o(2+1)5d


<?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="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>
 </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="2" />
 <child pos="1" />
 </linkage>
 </connection>
 </linkages>
 </sugar>

download coordinates

Corresponding entries: 13

1 - 5 of 13 entries with matching glycan part

Structure entry #373:

a-L-Fucp-(1-2)-b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-9)-9-hydroxy-Nonanoate-(1-1)-Methyl | a-L-Fucp-(1-3)+

13C: 1

: 6

Taxons

Structure entry #2037:

a-L-Fucp-(1-2)-b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-1)-<linker-TMR> | a-L-Fucp-(1-3)+

: 1

Taxons

Structure entry #2172: Lewis Y antigen, CD174

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

: 2

Taxons: 2

Structure entry #2546:

a-L-Fucp-(1-2)-b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-1)-?-3-en-4-deoxy-Hex-ol | a-L-Fucp-(1-3)+

: 2

Taxons

Structure entry #3805:

a-L-Fucp-(1-2)-b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-1)-Hex-3-en-1,2,5,6-tetrol | a-L-Fucp-(1-3)+

Taxons

Lewis Y (Show) (Search Database)

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General Structure Data

Chemical Formula:	C₂₆H₄₅N₁O₁₉	#C	#H	#O	#N
Molec. Weight:	675	26	45	19	1
# Atoms:	91
# Residues:	4
# Heavy Atoms:	46

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Composition

Superclasses:

Hex
Hex	1
dHex	2
HexNAc	1

Residues:

Residue	Count
A-L-FUCP	2
B-D-GALP	1
B-D-GLCPNAC	1

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PDB references: 7

1 - 5 of 7 PDB entries

PDB ID 5elc: Cholera toxin El Tor B-pentamer in complex with Lewis-y

Description: Cholera enterotoxin subunit B

Source: Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

Experimental method: X-RAY DIFFRACTION

Resolution: 1.5Å

Release date: 2016-03-30

Entry features 3 distinct glycan structures [10 instances].

PDB ID 4p25: Structure of the P domain from a GI.7 Norovirus variant in complex with LeY HBGA.

Description: Major capsid protein

Source: Norovirus Hu/GI.7/TCH-060/USA/2003

Experimental method: X-RAY DIFFRACTION

Resolution: 1.4991Å

Release date: 2014-04-02

Entry features 1 distinct glycan structures [4 instances].

PDB ID 4gwi: His 62 mutant of the lectin binding domain of lectinolysin complexed with Lewis y

Description: Platelet aggregation factor Sm-hPAF

Source: Streptococcus mitis

Experimental method: X-RAY DIFFRACTION

Resolution: 1.6Å

Release date: 2012-11-21

Entry features 1 distinct glycan structures [1 instances].

PDB ID 3pa2: Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with HBGA type Ley

Description: Capsid protein

Source: Norwalk virus

Experimental method: X-RAY DIFFRACTION

Resolution: 1.48Å

Release date: 2011-05-11

Entry features 1 distinct glycan structures [1 instances].

PDB ID 3leg: Lectin Domain of Lectinolysin complexed with Lewis Y Antigen

Description: Platelet aggregation factor Sm-hPAF

Source: Streptococcus mitis

Experimental method: X-RAY DIFFRACTION

Resolution: 2.01Å

Release date: 2010-12-29

Entry features 1 distinct glycan structures [1 instances].

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Literature references: 59

1 - 5 of 59 literature references

Reference #21957

Montesino B; Steenackers A; Lozano JM; Young GD; Hu N; Sackstein R; Chandler KB

Identification of α1,2-fucosylated signaling and adhesion molecules in head and neck squamous cell carcinoma.

Published 2022 in Glycobiology, 32: 441-455

Reference contains 4 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 #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 #21053

Gutiérrez-Huante K; Salinas-Marín R; Mora-Montes HM; Gonzalez RA; Martínez-Duncker I

Human adenovirus type 5 increases host cell fucosylation and modifies Ley antigen expression.

Published 2019 in Glycobiology, 29: 469-478

Reference contains 3 structures

Reference #21006

Gonciarz W; Walencka M; Moran AP; Hinc K; Obuchowski M; Chmiela M

Upregulation of MUC5AC production and deposition of LEWIS determinants by HELICOBACTER PYLORI facilitate gastric tissue colonization and the maintenance of infection.

Published 2019 in J. Biomed. Sci., 26: 23

Reference contains 2 structures

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Further literature references from PDB entries: 7

1 - 5 of 7 literature references from PDB entries

Reference #19530

Heggelund JE; Burschowsky D; Bjørnestad VA; Hodnik V; Anderluh G; Krengel U

High-Resolution Crystal Structures Elucidate the Molecular Basis of Cholera Blood Group Dependence.

Published 2016 in PLoS Pathog., 12: e1005567

Reference #18827

Shanker S; Czako R; Sankaran B; Atmar RL; Estes MK; Prasad BV

Structural analysis of determinants of histo-blood group antigen binding specificity in genogroup I noroviruses.

Published 2014 in J. Virol., 88: 6168-80

Reference #18359

Lawrence SL; Feil SC; Holien JK; Kuiper MJ; Doughty L; Dolezal O; Mulhern TD; Tweten RK; Parker MW

Manipulating the Lewis antigen specificity of the cholesterol-dependent cytolysin lectinolysin.

Published 2012 in Front Immunol, 3: 330

Reference #18095

Feil SC; Lawrence S; Mulhern TD; Holien JK; Hotze EM; Farrand S; Tweten RK; Parker MW

Structure of the lectin regulatory domain of the cholesterol-dependent cytolysin lectinolysin reveals the basis for its lewis antigen specificity.

Published 2012 in Structure, 20: 248-58

Reference #17837

Hansman GS; Biertümpfel C; Georgiev I; McLellan JS; Chen L; Zhou T; Katayama K; Kwong PD

Crystal structures of GII.10 and GII.12 norovirus protruding domains in complex with histo-blood group antigens reveal details for a potential site of vulnerability.

Published 2011 in J. Virol., 85: 6687-701

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Taxonomy: 6

NCBI Taxonomy ID	Scientific Name
9534	Cercopithecus aethiops
9606	Homo sapiens
12721	Human immunodeficiency virus
10090	Mus musculus
9986	Oryctolagus cuniculus
10114	Rattus

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Crosslinks: 6

Consortium for Functional Glycomics (CFG):

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Glycosciences.DB structure entry #1132: LewisY tetrasaccharide (beta-anomeric form)

1 - 5 of 13 entries with matching glycan part

1 - 5 of 7 PDB entries

1 - 5 of 59 literature references

1 - 5 of 7 literature references from PDB entries

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