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Glycosciences.DB structure entry #2677:

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Format: CarbBank LINUCS GlycoCT_condensed GlycoCT_xml


 b-D-Galp-(1-3)-b-D-GalpNAc-(1-4)+
                                 |
                            b-D-Galp-(1-4)-b-D-Glcp
                                 |
                a-D-Neup5Ac-(2-3)+


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


<?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="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="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>
 <substituent id="6" name="n-acetyl" />
 <basetype id="7" 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="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="2" />
 </linkage>
 </connection>
 <connection id="3" parent="3" child="4">
 <linkage id="3" parentType="d" childType="n">
 <parent pos="5" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="4" parent="2" 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="d" childType="n">
 <parent pos="2" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="6" parent="5" child="7">
 <linkage id="6" parentType="o" childType="d">
 <parent pos="3" />
 <child pos="1" />
 </linkage>
 </connection>
 </linkages>
 </sugar>

SNFG-style Graphics

3D Structure Model

download coordinates

Corresponding entries: 22

1 - 5 of 22 entries with matching glycan part

Structure entry #142: Glycosphingolipid GM1 / GM1a

b-D-Galp-(1-3)-b-D-GalpNAc-(1-4)+ | b-D-Galp-(1-4)-b-D-Glcp-(1-1)-Ceramide | a-D-Neup5Ac-(2-3)+

no 3d model

NMR spectra

literature references

no GlycoMaps

Structure entry #765:

b-D-Galp-(1-3)-b-D-GalpNAc-(1-4)+ | b-D-Galp-(1-4)-b-D-Glcp-(1-1)-<2-D-erythro-2-acetamide-octadec-4E-en-1,3-diol> | a-D-Neup5Ac-(2-3)+

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #766:

b-D-Galp-(1-3)-b-D-GalpNAc-(1-4)+ | b-D-Galp-(1-4)-b-D-Glcp-(1-1)-sphingosine-(2-1)-<2-chloroacetate> | a-D-Neup5Ac-(2-3)+

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #2875:

b-D-Galp-(1-3)-b-D-GalpNAc-(1-4)+ | b-D-Galp-(1-4)-b-D-Glcp-(1-1)-hexyl | a-D-Neup5Ac-(2-3)+

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #3946:

b-D-Galp-(1-3)-b-D-GalpNAc-(1-4)+ | b-D-Galp-(1-4)-b-D-Glcp-(1-1)-2R-amino-Octadec-4E-en-1,3S-diol | a-D-Neup5Ac-(2-3)+

no NMR spectra

literature references

no GlycoMaps

GM1a (Show) (Search Database)
GSL core, ganglio-type (Show) (Search Database)

General Structure Data

Chemical Formula:	C₃₇H₆₂N₂O₂₉		#C	#H	#O	#N
Molec. Weight:	998		37	62	29	2
# Atoms:	130
# Residues:	5
# Heavy Atoms:	68

Superclasses:

Neu		Hex
NeuAc	1	Hex	3
		HexNAc	1

Residues:

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

PDB references: 13

1 - 5 of 13 PDB entries

PDB ID 5n0c: Crystal structure of the tetanus neurotoxin in complex with GM1a

Description: Tetanus toxin (E.C.3.4.24.68)

Source: Clostridium tetani

Experimental method: X-RAY DIFFRACTION

Resolution: 2.6Å

Release date: 2017-06-21

Entry features 1 distinct glycan structures [2 instances].

PDB ID 4zh1: Complement factor H in complex with the GM1 glycan

Description: C3d, Complement factor H

Source: Homo sapiens

Experimental method: X-RAY DIFFRACTION

Resolution: 2.24Å

Release date: 2016-01-13

Entry features 3 distinct glycan structures [3 instances].

PDB ID 4u60: Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with GM1 oligosaccharide

Description: Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1

Source: Trichodysplasia spinulosa-associated polyomavirus

Experimental method: X-RAY DIFFRACTION

Resolution: 1.5Å

Release date: 2015-08-05

Entry features 3 distinct glycan structures [5 instances].

PDB ID 4x0z: JC Polyomavirus genotype 3 VP1 in complex with GM1 oligosaccharide

Description: JC polyomavirus VP1 from a genotype 3 strain

Source: JC polyomavirus type 3

Experimental method: X-RAY DIFFRACTION

Resolution: 1.85Å

Release date: 2015-04-22

Entry features 2 distinct glycan structures [3 instances].

PDB ID 4x14: JC Mad-1 polyomavirus VP1 in complex with GM1 oligosaccharide

Description: JC Mad-1 polyomavirus VP1

Source: JC polyomavirus

Experimental method: X-RAY DIFFRACTION

Resolution: 2.3Å

Release date: 2015-04-22

Entry features 2 distinct glycan structures [3 instances].

Literature references: 99

1 - 5 of 99 literature references

Reference #21775

Jayaprakash NG; Surolia A

Spike Protein and the Various Cell-Surface Carbohydrates: An Interaction Study.

Published 2021 in ACS Chem Biol, : epub ahead of print

Reference contains 32 structures

Reference #21776

Soares CO; Grosso AS; Ereño-Orbea J; Coelho H; Marcelo F

Molecular Recognition Insights of Sialic Acid Glycans by Distinct Receptors Unveiled by NMR and Molecular Modeling.

Published 2021 in Front Mol Biosci, 8: 727847

Reference contains 18 structures

Reference #20966

Grant OC; Tessier MB; Meche L; Mahal LK; Foley BL; Woods RJ

Combining 3D structure with glycan array data provides insight into the origin of glycan specificity.

Published 2016 in Glycobiology, 26: 772-783

Reference contains 22 structures

Reference #19426

Blaum BS; Frank M; Walker RC; Neu U; Stehle T

Complement Factor H and Simian Virus 40 bind the GM1 ganglioside in distinct conformations.

Published 2016 in Glycobiology, 26: 532-9

Reference contains 3 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: 8

1 - 5 of 8 literature references from PDB entries

Reference #19302

Ströh LJ; Gee GV; Blaum BS; Dugan AS; Feltkamp MC; Atwood WJ; Stehle T

Trichodysplasia spinulosa-Associated Polyomavirus Uses a Displaced Binding Site on VP1 to Engage Sialylated Glycolipids.

Published 2015 in PLoS Pathog., 11: e1005112

Reference #18676

Ng NM; Littler DR; Paton AW; Le Nours J; Rossjohn J; Paton JC; Beddoe T

EcxAB is a founding member of a new family of metalloprotease AB5 toxins with a hybrid cholera-like B subunit.

Published 2013 in Structure, 21: 2003-13

Reference #17729

Holmner A; Mackenzie A; Okvist M; Jansson L; Lebens M; Teneberg S; Krengel U

Crystal structures exploring the origins of the broader specificity of escherichia coli heat-labile enterotoxin compared to cholera toxin.

Published 2011 in J. Mol. Biol., 406: 387-402

Reference #17971

Bian CF; Zhang Y; Sun H; Li DF; Wang DC

Structural basis for distinct binding properties of the human galectins to Thomsen-Friedenreich antigen.

Published 2011 in PLoS ONE, 6: e25007

Reference #17568

Feng L; Sun H; Zhang Y; Li DF; Wang DC

Structural insights into the recognition mechanism between an antitumor galectin AAL and the Thomsen-Friedenreich antigen.

Published 2010 in FASEB J., 24: 3861-8

Consortium for Functional Glycomics (CFG):

carbSynthe_0629_D000

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