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Glycosciences.DB structure entry #229: N-Glycan fragment GlcNAc1

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Format: CarbBank LINUCS GlycoCT_xml


 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" />
 </residues>
 <linkages>
 <connection id="1" parent="1" child="2">
 <linkage id="1" 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: 48

1 - 5 of 48 entries with matching glycan part

Structure entry #556: O-GlcNAc linked to Ser

b-D-GlcpNAc-(1-3)-Ser

no NMR spectra

literature references

no GlycoMaps

Structure entry #588:

b-D-GlcpNAc-(1-3)+ | Ser-(1-2)-Ala | Gly-(1-2)+

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #594:

b-D-GlcpNAc-(1-4)+ | Asn-(1-2)-Gly-(1-2)-Ser-(1-2)-Met-(1-2)-Ser-(1-2)-Gly | Thr-(1-2)-His-(1-2)-Ala-(1-2)-Ser-(1-2)+

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #595:

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 #2038:

b-D-GlcpNAc-(1-1)-<linker-TMR>

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

N-GlcNAc
ENGase product

General Structure Data

Chemical Formula:	C₁₂H₂₁N₃O₇		#C	#H	#O	#N
Molec. Weight:	319		12	21	7	3
# Atoms:	43
# Residues:	2
# Heavy Atoms:	22

Superclasses:

Hex
HexNAc	1

Residues:

Residue	Count
ASN	1
B-D-GLCPNAC	1

NMR Proton Chemical Shift Info

MHz	360
Temperature	300
Solvent	D2O
Residue	Linkage	Proton	PPM	JFrom	JTo	Hz	Note
Asn		HA	3.968	a	b	6.9
Asn		HB	2.866	a	b'	4
Asn		HB'	2.932	b	b'	-17.8
b-D-GlcpNAc	4	H1	5.072	1	2	9.8
b-D-GlcpNAc	4	H2	3.821	2	3	10.6
b-D-GlcpNAc	4	H3	3.601	3	4	9.1
b-D-GlcpNAc	4	H4	3.472	4	5	10.4
b-D-GlcpNAc	4	H5	3.527	5	6	2.4
b-D-GlcpNAc	4	H6	3.876	5	6'	5.55
b-D-GlcpNAc	4	H6'	3.739	6	6'	-12.7
b-D-GlcpNAc	4	NAC	2.013			0

PDB references: 6680

1 - 5 of 6680 PDB entries

PDB ID 7f5q: An active enzyme from the plant Viola yedoensis

Description:

Source: Viola philippica

Experimental method: X-RAY DIFFRACTION

Resolution: 2.3Å

Release date: 2022-06-29

Entry features 3 distinct glycan structures [6 instances].

PDB ID 7f6y: Complex Structure of antibody BD-503 and RBD-E484K of COVID-19

Description:

Source: Severe acute respiratory syndrome coronavirus 2, HOMO SAPIENS

Experimental method: X-RAY DIFFRACTION

Resolution: 3Å

Release date: 2022-06-29

Entry features 1 distinct glycan structures [1 instances].

PDB ID 7y3u: Crystal structure of the complex of Lactoperoxidase with Nitric oxide at 2.50A resolution

Description:

Source: Bos grunniens

Experimental method: X-RAY DIFFRACTION

Resolution: 2.5Å

Release date: 2022-06-29

Entry features 2 distinct glycan structures [8 instances].

PDB ID 7zxu: SARS-CoV-2 Omicron BA.4/5 RBD in complex with Beta-27 Fab and C1 nanobody

Description:

Source: Severe acute respiratory syndrome coronavirus 2, Lama glama, HOMO SAPIENS

Experimental method: X-RAY DIFFRACTION

Resolution: 1.89Å

Release date: 2022-06-29

Entry features 1 distinct glycan structures [1 instances].

PDB ID 7f5j: a mutant of an enzyme from Viola yedoensis

Description:

Source: Viola philippica

Experimental method: X-RAY DIFFRACTION

Resolution: 1.593Å

Release date: 2022-06-29

Entry features 3 distinct glycan structures [6 instances].

Literature references: 16

1 - 5 of 16 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 #21197

Hobbs JK; Pluvinage B; Boraston AB

Glycan-metabolizing enzymes in microbe-host interactions: the Streptococcus pneumoniae paradigm.

Published 2018 in FEBS Lett., 592: 3865-3897

Reference contains 47 structures

Reference #20772

Li C; Li T; Wang LX

Chemoenzymatic Defucosylation of Therapeutic Antibodies for Enhanced Effector Functions Using Bacterial α-Fucosidases.

Published 2018 in Methods Mol. Biol., 1827: 367-380

Reference contains 2 structures

Reference #19000

Zouridakis M; Giastas P; Zarkadas E; Chroni-Tzartou D; Bregestovski P; Tzartos SJ

Crystal structures of free and antagonist-bound states of human α9 nicotinic receptor extracellular domain.

Published 2014 in Nat. Struct. Mol. Biol., 21: 976-80

Reference contains 1 structure

Reference #20487

Meuris L; Santens F; Elson G; Festjens N; Boone M; Dos Santos A; Devos S; Rousseau F; Plets E; Houthuys E; Malinge P; Magistrelli G; Cons L; Chatel L; Devreese B; Callewaert N

GlycoDelete engineering of mammalian cells simplifies N-glycosylation of recombinant proteins.

Published 2014 in Nat. Biotechnol., 32: 485-9

Reference contains 3 structures

Further literature references from PDB entries: 2198

1 - 5 of 2198 literature references from PDB entries

Reference #22016

Chi X; Guo Y; Zhang G; Sun H; Zhang J; Li M; Chen Z; Han J; Zhang Y; Zhang X; Fan P; Zhang Z; Wang B; Zai X; Han X; Hao M; Fang T; Xu J; Wu S; Chen Y; Fang Y; Dong Y; Sun B; Zhang J; Li J; Zhao G; Yu C; Zhou Q; Chen W

Broadly neutralizing antibodies against Omicron-included SARS-CoV-2 variants induced by vaccination.

Published 2022 in Signal Transduct Target Ther, 7: 139

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 #22025

Casasnovas JM; Margolles Y; Noriega MA; Guzmán M; Arranz R; Melero R; Casanova M; Corbera JA; Jiménez-de-Oya N; Gastaminza P; Garaigorta U; Saiz JC; Martín-Acebes MÁ; Fernández LÁ

Nanobodies Protecting From Lethal SARS-CoV-2 Infection Target Receptor Binding Epitopes Preserved in Virus Variants Other Than Omicron.

Published 2022 in Front Immunol, 13: 863831

Reference #21933

Sente A; Desai R; Naydenova K; Malinauskas T; Jounaidi Y; Miehling J; Zhou X; Masiulis S; Hardwick SW; Chirgadze DY; Miller KW; Aricescu AR

Differential assembly diversifies GABA receptor structures and signalling.

Published 2022 in Nature, 604: 190-194

Reference #21943

Ellis D; Lederhofer J; Acton OJ; Tsybovsky Y; Kephart S; Yap C; Gillespie RA; Creanga A; Olshefsky A; Stephens T; Pettie D; Murphy M; Sydeman C; Ahlrichs M; Chan S; Borst AJ; Park YJ; Lee KK; Graham BS; Veesler D; King NP; Kanekiyo M

Structure-based design of stabilized recombinant influenza neuraminidase tetramers.

Published 2022 in Nat Commun, 13: 1825

NCBI Taxonomy ID	Scientific Name
9606	Homo sapiens
12721	Human immunodeficiency virus
11309	unidentified influenza virus

Consortium for Functional Glycomics (CFG):

carbNlink_20379_D000

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