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Glycosciences.DB structure entry #3707: Lacto-N-difucohexaose I / LNDFH I (beta-anomeric form)

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Format: CarbBank LINUCS GlycoCT_condensed GlycoCT_xml


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


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-lgal-HEX-1:5|6:d
7b:a-lgal-HEX-1:5|6:d
LIN
1:1o(4+1)2d
2:2o(3+1)3d
3:3d(2+1)4n
4:3o(3+1)5d
5:5o(2+1)6d
6:3o(4+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="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="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="7" 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="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="3" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="5" parent="5" child="6">
 <linkage id="5" parentType="o" childType="d">
 <parent pos="2" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="6" parent="3" child="7">
 <linkage id="6" parentType="o" childType="d">
 <parent pos="4" />
 <child pos="1" />
 </linkage>
 </connection>
 </linkages>
 </sugar>

SNFG-style Graphics

3D Structure Model

download coordinates

Corresponding entries: 3

1 - 3 of 3 entries with matching glycan part

Structure entry #689: Lewis B Hexaosylceramide

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

no 3d model

no NMR spectra

literature references

no GlycoMaps

Structure entry #15459:

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

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #17661:

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

no NMR spectra

literature references

no GlycoMaps

Taxons

Lewis B (Show) (Search Database)
Lewis D internal (Show) (Search Database)
GSL core, lacto-type (Show) (Search Database)

lacto-N-difucohexaose I
LNDFH I

Human milk oligosaccharide
HMO

General Structure Data

Chemical Formula:	C₃₈H₆₅N₁O₂₉		#C	#H	#O	#N
Molec. Weight:	999		38	65	29	1
# Atoms:	133
# Residues:	6
# Heavy Atoms:	68

Superclasses:

Hex
Hex	3
dHex	2
HexNAc	1

Residues:

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

PDB references: 5

1 - 5 of 5 PDB entries

PDB ID 7khu: Crystal structure of the carbohydrate-binding domain VP8* of human P[4] rotavirus strain BM5265 in complex with LNDFH I

Description:

Source: Human rotavirus A

Experimental method: X-RAY DIFFRACTION

Resolution: 2.54Å

Release date: 2021-08-18

Entry features 1 distinct glycan structures [2 instances].

PDB ID 7jhz: Crystal structure of the carbohydrate-binding domain VP8* of human P[8] rotavirus strain BM13851 in complex with LNDFH I

Description:

Source: Human rotavirus A

Experimental method: X-RAY DIFFRACTION

Resolution: 2.68Å

Release date: 2021-07-28

Entry features 2 distinct glycan structures [2 instances].

PDB ID 5f7m: Blood group antigen binding adhesin BabA of Helicobacter pylori strain 17875 in complex with blood group H Lewis b hexasaccharide

Description: Adhesin binding fucosylated histo-blood group antigen, Nanobody Nb-ER19

Source: Helicobacter pylori, Lama glama

Experimental method: X-RAY DIFFRACTION

Resolution: 2.72Å

Release date: 2016-01-20

Entry features 1 distinct glycan structures [2 instances].

PDB ID 5f8r: Blood group antigen binding adhesin BabA of Helicobacter pylori strain S831 in complex with blood group H Lewis b hexasaccharide

Description: Adhesin binding fucosylated histo-blood group antigen, Nanobody Nb-ER19

Source: Helicobacter pylori, Lama glama

Experimental method: X-RAY DIFFRACTION

Resolution: 2.44Å

Release date: 2016-01-20

Entry features 1 distinct glycan structures [2 instances].

PDB ID 3sej: Structural characterization of a GII.4 2004 norovirus variant (TCH05) bound to Secretor Lewis HBGA (LeB)

Description: Capsid

Source: Norovirus Hu/GII.4/2004/NL

Experimental method: X-RAY DIFFRACTION

Resolution: 3.041Å

Release date: 2011-07-13

Entry features 1 distinct glycan structures [8 instances].

Literature references: 3

1 - 3 of 3 literature references

Reference #20959

Guberman M; Seeberger PH

Automated Glycan Assembly: A Perspective.

Published 2019 in J. Am. Chem. Soc., 141: 5581-5592

Reference contains 59 structures

Reference #19438

Moonens K; Gideonsson P; Subedi S; Bugaytsova J; Romaõ E; Mendez M; Nordén J; Fallah M; Rakhimova L; Shevtsova A; Lahmann M; Castaldo G; Brännström K; Coppens F; Lo AW; Ny T; Solnick JV; Vandenbussche G; Oscarson S; Hammarström L; Arnqvist A; Berg D

Structural Insights into Polymorphic ABO Glycan Binding by Helicobacter pylori.

Published 2016 in Cell Host Microbe, 19: 55-66

Reference contains 6 structures

Reference #1495

Blood group-related oligosaccharides are ligands in cell-adhesion events

Published 1992 in Biochem Soc Trans, 20: 274-278

Reference contains 10 structures

Further literature references from PDB entries: 1

1 - 1 of 1 literature references from PDB entries

Reference #17898

Shanker S; Choi JM; Sankaran B; Atmar RL; Estes MK; Prasad BV

Structural analysis of histo-blood group antigen binding specificity in a norovirus GII.4 epidemic variant: implications for epochal evolution.

Published 2011 in J. Virol., 85: 8635-45

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