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Glycosciences.DB structure entry #16145:

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Format: CarbBank LINUCS GlycoCT_xml


                a-D-Manp-(1-6)+
                              |
                         b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-Asn
                              |
 a-D-Manp-(1-2)-a-D-Manp-(1-3)+


<?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>
 <basetype id="6" anomer="a" superclass="hex" ringStart="1" ringEnd="5" name="a-dman-HEX-1:5">
 <stemtype id="1" type="dman" />
 </basetype>
 <basetype id="7" anomer="a" superclass="hex" ringStart="1" ringEnd="5" name="a-dman-HEX-1:5">
 <stemtype id="1" type="dman" />
 </basetype>
 <basetype id="8" anomer="a" superclass="hex" ringStart="1" ringEnd="5" name="a-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>
 <connection id="5" parent="5" child="6">
 <linkage id="5" parentType="o" childType="d">
 <parent pos="3" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="6" parent="6" child="7">
 <linkage id="6" parentType="o" childType="d">
 <parent pos="2" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="7" parent="5" child="8">
 <linkage id="7" parentType="o" childType="d">
 <parent pos="6" />
 <child pos="1" />
 </linkage>
 </connection>
 </linkages>
 <aglyca>
 <historicalData>
 <entry id="0" name="ASN" toResidue="1">
 <linkage parentType="n" childType="x">
 <parent pos="4" />
 <child pos="1" />
 </linkage>
 </entry>
 </historicalData>
 </aglyca>
 </sugar>

SNFG-style Graphics

3D Structure Model

download coordinates

Corresponding entries: 1

1 - 1 of 1 entries with matching glycan part

Structure entry #23252:

a-D-Manp-(1-6)+ | b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc | a-D-Manp-(1-2)-a-D-Manp-(1-3)+

no NMR spectra

literature references

no GlycoMaps

Taxons

N-glycan core (Show) (Search Database)

General Structure Data

Chemical Formula:	C₄₄H₇₄N₄O₃₂		#C	#H	#O	#N
Molec. Weight:	1170		44	74	32	4
# Atoms:	154
# Residues:	7
# Heavy Atoms:	80

Superclasses:

Hex
Hex	4
HexNAc	2

Residues:

Residue	Count
A-D-MANP	3
ASN	1
B-D-GLCPNAC	2
B-D-MANP	1

PDB references: 104

1 - 5 of 104 PDB entries

PDB ID 8b3b: Structure of metacyclic VSG (mVSG) 531 from Trypanosoma brucei

Description:

Source: Trypanosoma brucei

Experimental method: X-RAY DIFFRACTION

Resolution: 1.949Å

Release date: 2023-01-25

Entry features 4 distinct glycan structures [8 instances].

PDB ID 8bet: Structure of D188A-fructofuranosidase from Rhodotorula dairenesis in complex with sucrose

Description:

Source: Rhodotorula dairenensis

Experimental method: X-RAY DIFFRACTION

Resolution: 2.38Å

Release date: 2022-12-28

Entry features 7 distinct glycan structures [51 instances].

PDB ID 7uot: Native Lassa glycoprotein in complex with neutralizing antibodies 8.9F and 37.2D

Description:

Source: Lassa virus, Homo sapiens

Experimental method: ELECTRON MICROSCOPY

Release date: 2022-11-02

Entry features 8 distinct glycan structures [33 instances].

PDB ID 7uov: Native Lassa glycoprotein in complex with neutralizing antibodies 12.1F and 37.2D

Description:

Source: Homo sapiens, Lassa virus

Experimental method: ELECTRON MICROSCOPY

Release date: 2022-11-02

Entry features 7 distinct glycan structures [33 instances].

PDB ID 7t2p: The Envelope Glycoprotein SIVmac239.K180S SOSIP trimer in complex with 3 copies of the neutralizing antibody K11

Description:

Source: Simian immunodeficiency virus, Macaca mulatta

Experimental method: ELECTRON MICROSCOPY

Release date: 2022-10-19

Entry features 7 distinct glycan structures [25 instances].

Literature references: 2

1 - 2 of 2 literature references

Reference #9459

Nilsson B; Nakazawa K; Hassell JR; Newsome DA; Hascall VC

Structure of oligosaccharides and the linkage region between keratan sulfate and the core protein on proteoglycans from monkey cornea

Published 1983 in J Biol Chem, 258: 6056-6063

Reference contains 3 structures

Reference #9327

Kornfeld S; Gregory W; Chapman A

Class E Thy-1 negative mouse lymphoma cells utilize an alternate pathway of oligosaccharide processing to synthesize complex-type oligosaccharides

Published 1979 in J Biol Chem, 254: 11649-11654

Reference contains 9 structures

Further literature references from PDB entries: 51

1 - 5 of 51 literature references from PDB entries

Reference #22602

Jiménez-Ortega E; Narmontaite E; González-Pérez B; Plou FJ; Fernández-Lobato M; Sanz-Aparicio J

Insights into the Structure of the Highly Glycosylated Ffase from Enhance Its Biotechnological Potential.

Published 2022 in Int J Mol Sci, 23:

Reference #21929

Gao N; Gai Y; Meng L; Wang C; Wang W; Li X; Gu T; Louder MK; Doria-Rose NA; Wiehe K; Nazzari AF; Olia AS; Gorman J; Rawi R; Wu W; Smith C; Khant H; de Val N; Yu B; Luo J; Niu H; Tsybovsky Y; Liao H; Kepler TB; Kwong PD; Mascola JR; Qin C; Zhou T; Yu X; G

Development of Neutralization Breadth against Diverse HIV-1 by Increasing Ab-Ag Interface on V2.

Published 2022 in Adv Sci (Weinh), : e2200063

Reference #22521

Zhao F; Berndsen ZT; Pedreño-Lopez N; Burns A; Allen JD; Barman S; Lee WH; Chakraborty S; Gnanakaran S; Sewall LM; Ozorowski G; Limbo O; Song G; Yong P; Callaghan S; Coppola J; Weisgrau KL; Lifson JD; Nedellec R; Voigt TB; Laurino F; Louw J; Rosen BC; R

Molecular insights into antibody-mediated protection against the prototypic simian immunodeficiency virus.

Published 2022 in Nat Commun, 13: 5236

Reference #22537

Li H; Buck T; Zandonatti M; Yin J; Moon-Walker A; Fang J; Koval A; Heinrich ML; Rowland MM; Diaz Avalos R; Schendel SL; Parekh D; Zyla D; Enriquez A; Harkins S; Sullivan B; Smith V; Chukwudozie O; Watanabe R; Robinson JE; Garry RF; Branco LM; Hastie KM;

A cocktail of protective antibodies subverts the dense glycan shield of Lassa virus.

Published 2022 in Sci Transl Med, 14: eabq0991

Reference #21443

Jette CA; Barnes CO; Kirk SM; Melillo B; Smith AB; Bjorkman PJ

Cryo-EM structures of HIV-1 trimer bound to CD4-mimetics BNM-III-170 and M48U1 adopt a CD4-bound open conformation.

Published 2021 in Nat Commun, 12: 1950

NCBI Taxonomy ID	Scientific Name
10090	Mus musculus
9443	Primates

Consortium for Functional Glycomics (CFG):

carbNlink_20464_D000

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