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Glycosciences.DB structure entry #548: N-Glycan fragment GlcNAc2

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Format: CarbBank LINUCS GlycoCT_xml


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


<?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" />
 </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>
 </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: 18

1 - 5 of 18 entries with matching glycan part

Structure entry #552:

b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-Asn-(1-2)-Phe-(1-2)-Thr

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #553:

b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-Asn-(1-2)-Ala-(1-2)-Thr-(1-2)-Ala-(1-2)-Ser

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #596:

b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)+ | Asn-(1-2)-Lys-(1-2)-Thr-(1-2)-Leu-(1-2)-Met | Gly-(1-2)-Lys-(1-2)-Ala-(1-2)-Tyr-(1-2)-Thr-(1-2)-Ile-(1-2)-Phe-(1-2)+

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #1928:

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

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #2209:

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

General Structure Data

Chemical Formula:	C₂₀H₃₄N₄O₁₂		#C	#H	#O	#N
Molec. Weight:	522		20	34	12	4
# Atoms:	70
# Residues:	3
# Heavy Atoms:	36

Superclasses:

Hex
HexNAc	2

Residues:

Residue	Count
ASN	1
B-D-GLCPNAC	2

PDB references: 4263

1 - 5 of 4263 PDB entries

PDB ID 7ued: Crystal structure of full length mesothelin bound with MORAb-009 Fab

Description:

Source: Homo sapiens, Mus musculus

Experimental method: X-RAY DIFFRACTION

Resolution: 3Å

Release date: 2023-02-01

Entry features 1 distinct glycan structures [1 instances].

PDB ID 7wrh: Cryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in complex with mouse ACE2

Description:

Source: Severe acute respiratory syndrome coronavirus 2, Homo sapiens

Experimental method: ELECTRON MICROSCOPY

Release date: 2023-02-01

Entry features 2 distinct glycan structures [45 instances].

PDB ID 7ysg: Cryo-EM structure of human FcmR bound to sIgM

Description:

Source: HOMO SAPIENS, Homo sapiens

Experimental method: ELECTRON MICROSCOPY

Release date: 2023-02-01

Entry features 3 distinct glycan structures [11 instances].

PDB ID 8c6i: TMEM2 ectodomain

Description:

Source: Homo sapiens

Experimental method: X-RAY DIFFRACTION

Resolution: 3.5Å

Release date: 2023-02-01

Entry features 6 distinct glycan structures [9 instances].

PDB ID 8cx3: Crystal structure of full-length mesothelin

Description:

Source: Homo sapiens

Experimental method: X-RAY DIFFRACTION

Resolution: 3.609Å

Release date: 2023-02-01

Entry features 3 distinct glycan structures [6 instances].

Literature references: 6

1 - 5 of 6 literature references

Reference #21726

Tjondro HC; Ugonotti J; Kawahara R; Chatterjee S; Loke I; Chen S; Soltermann F; Hinneburg H; Parker BL; Venkatakrishnan V; Dieckmann R; Grant OC; Bylund J; Rodger A; Woods RJ; Karlsson-Bengtsson A; Struwe WB; Thaysen-Andersen M

Hyper-truncated Asn355- and Asn391-glycans modulate the activity of neutrophil granule myeloperoxidase.

Published 2021 in J Biol Chem, 296: 100144

Reference contains 20 structures

Reference #21166

Bello-Gil D; Audebert C; Olivera-Ardid S; Pérez-Cruz M; Even G; Khasbiullina N; Gantois N; Shilova N; Merlin S; Costa C; Bovin N; Mañez R

The Formation of Glycan-Specific Natural Antibodies Repertoire in GalT-KO Mice Is Determined by Gut Microbiota.

Published 2019 in Front Immunol, 10: 342

Reference contains 32 structures

Garg HG; Von dem Bruch K; Kunz H

Developments in the synthesis of glycopeptides containing glycosyl L-asparagine, L-serine, and L-threonine

Published 1994 in Adv Carbohydr Chem Biochem, 50: 277-310

Reference contains 59 structures

Reference #1363

Piskarev VE; Navratil J; Karaskova H; Bezouska K; Kocourek J

Interaction of egg-white glycoproteins and their oligosaccharides with the monomer and the hexamer of chicken liver lectin

Published 1990 in Biochem J, 270: 755-760

Reference contains 14 structures

Reference #3606

Nomoto H; Endo T; Inoue Y

Preparation and characterization of fragment glycoasparagines from ovalbumin glycopeptides: reference compounds for structural and biochemical studies of the oligo-mannose and hybrid types of carbohydrate chains of glycoproteins

Published 1982 in Carbohydr Res, 107: 91-101

Reference contains 9 structures

Further literature references from PDB entries: 1501

1 - 5 of 1501 literature references from PDB entries

Reference #22684

Saville JW; Mannar D; Zhu X; Berezuk AM; Cholak S; Tuttle KS; Vahdatihassani F; Subramaniam S

Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein.

Published 2023 in Cell Rep, 42: 111964

Reference #22705

Huang KA; Chen X; Mohapatra A; Nguyen HTV; Schimanski L; Tan TK; Rijal P; Vester SK; Hills RA; Howarth M; Keeffe JR; Cohen AA; Kakutani LM; Wu YM; Shahed-Al-Mahmud M; Chou YC; Bjorkman PJ; Townsend AR; Ma C

Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.

Published 2023 in Nat Commun, 14: 311

Reference #22685

Le Floc'h A; Nagashima K; Birchard D; Scott G; Ben LH; Ajithdoss D; Gayvert K; Romero Hernandez A; Herbin O; Tay A; Farrales P; Korgaonkar CK; Pan H; Shah S; Kamat V; Chatterjee I; Popke J; Oyejide A; Lim WK; Kim JH; Huang T; Franklin M; Olson W; Norton

Blocking common γ chain cytokine signaling ameliorates T cell-mediated pathogenesis in disease models.

Published 2023 in Sci Transl Med, 15: eabo0205

Reference #22683

Bianchini F; Crivelli V; Abernathy ME; Guerra C; Palus M; Muri J; Marcotte H; Piralla A; Pedotti M; Gasparo R; Simonelli L; Matkovic M; Toscano C; Biggiogero M; Calvaruso V; Svoboda P; Rincón TC; Fava T; Podešvová L; Shanbhag AA; Celoria A; Sgrignani

Human neutralizing antibodies to cold linear epitopes and to subdomain 1 of SARS-CoV-2.

Published 2022 in bioRxiv, :

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

NCBI Taxonomy ID	Scientific Name
9913	Bos taurus

Consortium for Functional Glycomics (CFG):

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