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Glycosciences.DB structure entry #3821:

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Format: CarbBank LINUCS GlycoCT_condensed GlycoCT_xml


 b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc


RES
1b:b-dglc-HEX-1:5
2s:n-acetyl
3b:b-dglc-HEX-1:5
4s:n-acetyl
5b:b-dman-HEX-1:5
LIN
1:1d(2+1)2n
2:1o(4+1)3d
3:3d(2+1)4n
4:3o(4+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="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-dman-HEX-1:5">
 <stemtype id="1" type="dman" />
 </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="4" />
 <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="4" />
 <child pos="1" />
 </linkage>
 </connection>
 </linkages>
 </sugar>

SNFG-style Graphics

3D Structure Model

download coordinates

Corresponding entries: 8

1 - 5 of 8 entries with matching glycan part

Structure entry #551: N-Glycan fragment GlcNAc2Man1

b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-Asn

no NMR spectra

literature references

no GlycoMaps

Structure entry #3409:

b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-Asn-(2-1)-Acetate

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #5704:

b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-7)-<7-amino-4-methyl-2h-1-benzopyran-2-one>

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #13373:

b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)+ | Asn-(1-2)-Tyr-(1-2)-Thr | octanoate-(1-2)+

no NMR spectra

literature references

no GlycoMaps

Structure entry #13729:

b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-O)-dolichol-PP

no NMR spectra

literature references

no GlycoMaps

General Structure Data

Chemical Formula:	C₂₂H₃₈N₂O₁₆		#C	#H	#O	#N
Molec. Weight:	586		22	38	16	2
# Atoms:	78
# Residues:	3
# Heavy Atoms:	40

Superclasses:

Hex
Hex	1
HexNAc	2

Residues:

Residue	Count
B-D-GLCPNAC	2
B-D-MANP	1

PDB references: 2

1 - 2 of 2 PDB entries

PDB ID 6zp5: SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up closed conformation)

Description: Spike glycoprotein

Source: Severe acute respiratory syndrome coronavirus 2

Experimental method: ELECTRON MICROSCOPY

Release date: 2020-07-29

Entry features 6 distinct glycan structures [46 instances].

PDB ID 6zp7: SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up open conformation)

Description: Spike glycoprotein

Source: Severe acute respiratory syndrome coronavirus 2

Experimental method: ELECTRON MICROSCOPY

Release date: 2020-07-29

Entry features 6 distinct glycan structures [46 instances].

Conformational maps: 6

Map ID: 8783

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

Linkage Path: 44

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

Map ID: 8784

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

Linkage Path: 4

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

Map ID: 8808

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

Linkage Path: 44

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

Map ID: 8809

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

Linkage Path: 4

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

Map ID: 9353

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

Linkage Path: 44

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

Map ID: 9354

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

Linkage Path: 4

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

Literature references: 7

1 - 5 of 7 literature references

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 #20687

Harbison AM; Brosnan LP; Fenlon K; Fadda E

Sequence-to-structure dependence of isolated IgG Fc complex biantennary N-glycans: a molecular dynamics study.

Published 2019 in Glycobiology, 29: 94-103

Reference contains 20 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 #6770

Joao HC; Dwek RA

Effects of glycosylation on protein structure and dynamics in ribonuclease B and some of its individual glycoforms

Published 1993 in Eur J Biochem, 218: 239-244

Reference contains 2 structures

Reference #7462

Cacan R; Villers C; Belard M; Kaiden A; Krag SS; Verbert A

Different fates of the oligosaccharide moieties of lipid intermediates

Published 1992 in Glycobiology, 2: 127-136

Reference contains 1 structure

Further literature references from PDB entries: 1

1 - 1 of 1 literature references from PDB entries

Reference #22263

Melero R; Sorzano COS; Foster B; Vilas JL; Martínez M; Marabini R; Ramírez-Aportela E; Sanchez-Garcia R; Herreros D; Del Caño L; Losana P; Fonseca-Reyna YC; Conesa P; Wrapp D; Chacon P; McLellan JS; Tagare HD; Carazo JM

Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures.

Published 2020 in bioRxiv, :

NCBI Taxonomy ID	Scientific Name
10029	Cricetulus griseus

Consortium for Functional Glycomics (CFG):

carbNlink_40450_D000

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