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Glycosciences.DB structure entry #50: Lewis X trisaccharide (beta-anomeric form)

Format: CarbBank LINUCS GlycoCT_condensed GlycoCT_xml


 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
LIN
1:1d(2+1)2n
2:1o(3+1)3d
3:1o(4+1)4d


<?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>
 </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>
 </linkages>
 </sugar>

download coordinates

Corresponding entries: 14

1 - 5 of 14 entries with matching glycan part

Structure entry #369:

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

13C: 1

: 3

Taxons

Structure entry #2036:

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

: 1

Taxons

Structure entry #2174: Lewis X antigen, CD15

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

: 3

Taxons: 3

Structure entry #2217:

: 1

Taxons

Structure entry #4554:

b-D-Galp-(1-4)+ | b-D-GlcpNAc-(1-7)-benzyl | a-L-Fucp-(1-3)+

Taxons

Lewis X (Show) (Search Database)

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Trivial names

LewisX
LeX
CD15
Lewis-X
Le-X
Lewis X

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General Structure Data

Chemical Formula:	C₂₀H₃₅N₁O₁₅	#C	#H	#O	#N
Molec. Weight:	529	20	35	15	1
# Atoms:	71
# Residues:	3
# Heavy Atoms:	36

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Composition

Superclasses:

Hex
Hex	1
dHex	1
HexNAc	1

Residues:

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

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PDB references: 7

1 - 5 of 7 PDB entries

PDB ID 6hjd: Cholera toxin classical B-pentamer in complex with Lewis-x

Description: Cholera toxin B subunit

Source: Vibrio cholerae

Experimental method: X-RAY DIFFRACTION

Resolution: 1.54Å

Release date: 2019-08-14

Entry features 3 distinct glycan structures [9 instances].

PDB ID 6r35: Structure of the LecB lectin from Pseudomonas aeruginosa strain PAO1 in complex with lewis x tetrasaccharide

Description: Fucose-binding lectin PA-IIL

Source: Pseudomonas aeruginosa PAO1

Experimental method: X-RAY DIFFRACTION

Resolution: 1.8Å

Release date: 2019-06-12

Entry features 1 distinct glycan structures [4 instances].

PDB ID 5o7u: Crystal structure of the 7-Fluorotryptophan RSL lectin in complex with Lewis x tetrasaccharide

Description: Putative fucose-binding lectin protein

Source: Ralstonia solanacearum

Experimental method: X-RAY DIFFRACTION

Resolution: 1.15Å

Release date: 2018-06-06

Entry features 4 distinct glycan structures [4 instances].

PDB ID 5o7v: Crystal structure of the 5F-tryptophan RSL lectin in complex with Lewis x tetrasaccharide

Description: Putative fucose-binding lectin protein

Source: Ralstonia solanacearum

Experimental method: X-RAY DIFFRACTION

Resolution: 1.28Å

Release date: 2018-06-06

Entry features 3 distinct glycan structures [4 instances].

PDB ID 5ajb: X-ray structure of the RSL lectin in complex with Lewis X tetrasaccahride

Description: LECTIN

Source: RALSTONIA SOLANACEARUM

Experimental method: X-RAY DIFFRACTION

Resolution: 1.8Å

Release date: 2016-03-02

Entry features 3 distinct glycan structures [5 instances].

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Conformational maps: 2

Map ID: 8431

Disaccharide Fragment: a-L-Fucp-(1-3)-b-D-GlcpNAc

Linkage Path: 3

Method: MD MM3(1996) Tinker 4 HTMD, 1000K, 30ns

details...

Map ID: 8432

Disaccharide Fragment: b-D-Galp-(1-4)-b-D-GlcpNAc

Linkage Path: 4

Method: MD MM3(1996) Tinker 4 HTMD, 1000K, 30ns

details...

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Literature references: 136

1 - 5 of 136 literature references

Reference #22029

Klarić TS; Lauc G

The dynamic brain N-glycome.

Published 2022 in Glycoconj J, 39: 443-471

Reference contains 18 structures

Reference #21964

Brockhausen I; Schutzbach J; Wang J; Fishwick B; Brockhausen J

Glycoconjugate journal special issue on: the glycobiology of Parkinson's disease.

Published 2022 in Glycoconj J, 39: 55-74

Reference contains 9 structures

Reference #21648

Robakiewicz S; Bridot C; Serna S; Gimeno A; Echeverria B; Delgado S; de Ruyck J; Semwal S; Charro D; Dansercoer A; Verstraete K; Azkargorta M; van Noort K; Wilbers RHP; Savvides SN; Abrescia NGA; Arda A; Reichardt NC; Jiménez-Barbero J; Bouckaert J

Minimal epitope for Mannitou IgM on paucimannose-carrying glycoproteins.

Published 2021 in Glycobiology, 31: 1005-1017

Reference contains 29 structures

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 #21750

Kudelka MR; Stowell SR; Cummings RD; Neish AS

Intestinal epithelial glycosylation in homeostasis and gut microbiota interactions in IBD.

Published 2020 in Nat Rev Gastroenterol Hepatol, 17: 597-617

Reference contains 35 structures

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Further literature references from PDB entries: 2

1 - 2 of 2 literature references from PDB entries

Reference #21145

Lepsik M; Sommer R; Kuhaudomlarp S; Lelimousin M; Paci E; Varrot A; Titz A; Imberty A

Induction of rare conformation of oligosaccharide by binding to calcium-dependent bacterial lectin: X-ray crystallography and modelling study.

Published 2019 in Eur J Med Chem, 177: 212-220

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

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Taxonomy: 10

NCBI Taxonomy ID	Scientific Name
10141	Cavia porcellus
9534	Cercopithecus aethiops
10029	Cricetulus griseus
9031	Gallus gallus
9606	Homo sapiens
10090	Mus musculus
8638	Naja
9986	Oryctolagus cuniculus
10114	Rattus
6183	Schistosoma mansoni

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Crosslinks: 7

Consortium for Functional Glycomics (CFG):

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Glycosciences.DB structure entry #50: Lewis X trisaccharide (beta-anomeric form)

1 - 5 of 14 entries with matching glycan part

1 - 5 of 7 PDB entries

1 - 5 of 136 literature references

1 - 2 of 2 literature references from PDB entries

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