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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: 7675

1 - 5 of 7675 PDB entries

PDB ID 8hhx: SARS-CoV-2 Delta Spike in complex with FP-12A

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 [28 instances].

PDB ID 8hhy: SARS-CoV-2 Delta Spike in complex with IS-9A

Description:

Source: HOMO SAPIENS, Severe acute respiratory syndrome coronavirus 2

Experimental method: ELECTRON MICROSCOPY

Release date: 2023-02-01

Entry features 2 distinct glycan structures [28 instances].

PDB ID 8dmk: Cryo-EM reveals the molecular basis of laminin polymerization and LN-lamininopathies

Description:

Source: Homo sapiens, Mus musculus

Experimental method: ELECTRON MICROSCOPY

Release date: 2023-02-01

Entry features 1 distinct glycan structures [4 instances].

PDB ID 7ttz: Heterodimeric IgA Fc in complex with Staphylococcus aureus protein SSL7

Description:

Source: Homo sapiens, STAPHYLOCOCCUS AUREUS

Experimental method: X-RAY DIFFRACTION

Resolution: 2.35Å

Release date: 2023-02-01

Entry features 1 distinct glycan structures [1 instances].

PDB ID 7wr9: Local CryoEM structure of the SARS-CoV S2P in complex with BD55-3152 Fab

Description:

Source: HOMO SAPIENS, Severe acute respiratory syndrome coronavirus

Experimental method: ELECTRON MICROSCOPY

Release date: 2023-02-01

Entry features 2 distinct glycan structures [2 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 #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

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

Further literature references from PDB entries: 2512

1 - 5 of 2512 literature references from PDB entries

Reference #22611

Tandrup T; Lo Leggio L; Meilleur F

Joint X-ray/neutron structure of Lentinus similis AA9_A at room temperature.

Published 2023 in Acta Crystallogr F Struct Biol Commun, 79: 1-7

Reference #22625

Troisi R; Galardo F; Ferraro G; Sica F; Merlino A

Cisplatin Binding to Human Serum Transferrin: A Crystallographic Study.

Published 2023 in Inorg Chem, 62: 675-678

Reference #22706

Meden A; Knez D; Brazzolotto X; Modeste F; Perdih A; Pišlar A; Zorman M; Zorović M; Denic M; Pajk S; Živin M; Nachon F; Gobec S

Pseudo-irreversible butyrylcholinesterase inhibitors: Structure-activity relationships, computational and crystallographic study of the N-dialkyl O-arylcarbamate warhead.

Published 2023 in Eur J Med Chem, 247: 115048

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 #22704

Ge Q; Teng M; Li X; Guo Q; Tao Y

An epitope-directed selection strategy facilitating the identification of Frizzled receptor selective antibodies.

Published 2023 in Structure, 31: 33-43.e5

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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