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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: 7497

1 - 5 of 7497 PDB entries

PDB ID 7uny: Crystal structure of D2 nanobody in complex with PfCSS

Description:

Source: Plasmodium falciparum, Vicugna pacos

Experimental method: X-RAY DIFFRACTION

Resolution: 4.13Å

Release date: 2022-11-23

Entry features 3 distinct glycan structures [7 instances].

PDB ID 7unz: Crystal structure of H2 nanobody in complex with PfCSS

Description:

Source: Plasmodium falciparum, Vicugna pacos

Experimental method: X-RAY DIFFRACTION

Resolution: 2.03Å

Release date: 2022-11-23

Entry features 3 distinct glycan structures [10 instances].

PDB ID 7xmx: Cryo-EM structure of SARS-CoV-2 spike glycoprotein in complex with three F61 Fab

Description:

Source: Severe acute respiratory syndrome coronavirus 2, HOMO SAPIENS

Experimental method: ELECTRON MICROSCOPY

Release date: 2022-11-23

Entry features 1 distinct glycan structures [24 instances].

PDB ID 7xmz: Cryo-EM structure of SARS-CoV-2 spike glycoprotein in complex with three D2 Fab

Description:

Source: Severe acute respiratory syndrome coronavirus 2, HOMO SAPIENS

Experimental method: ELECTRON MICROSCOPY

Release date: 2022-11-23

Entry features 1 distinct glycan structures [32 instances].

PDB ID 7xst: Cryo-EM structure of SARS-CoV-2 Omicron spike glycoprotein in complex with three F61 Fab and three D2 Fab

Description:

Source: Severe acute respiratory syndrome coronavirus 2, HOMO SAPIENS

Experimental method: ELECTRON MICROSCOPY

Release date: 2022-11-23

Entry features 1 distinct glycan structures [31 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 #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 #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 #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: 2474

1 - 5 of 2474 literature references from PDB entries

Reference #22558

Nan J; Yuan Y; Yang X; Shan Z; Liu H; Wei F; Zhang W; Zhang Y

Cryo-EM structure of the human sodium-chloride cotransporter NCC.

Published 2022 in Sci Adv, 8: eadd7176

Reference #22522

Huang X; Wang Y; Yu C; Zhang H; Ru Q; Li X; Song K; Zhou M; Zhu P

Cryo-EM structures reveal the dynamic transformation of human alpha-2-macroglobulin working as a protease inhibitor.

Published 2022 in Sci China Life Sci, :

Reference #22453

Barnes CO; Schoofs T; Gnanapragasam PNP; Golijanin J; Huey-Tubman KE; Gruell H; Schommers P; Suh-Toma N; Lee YE; Cetrulo Lorenzi JC; Piechocka-Trocha A; Scheid JF; West AP; Walker BD; Seaman MS; Klein F; Nussenzweig MC; Bjorkman PJ

A naturally arising broad and potent CD4-binding site antibody with low somatic mutation.

Published 2022 in Sci Adv, 8: eabp8155

Reference #22393

Vourloumis D; Mavridis I; Athanasoulis A; Temponeras I; Koumantou D; Giastas P; Mpakali A; Magrioti V; Leib J; van Endert P; Stratikos E; Papakyriakou A

Discovery of Selective Nanomolar Inhibitors for Insulin-Regulated Aminopeptidase Based on α-Hydroxy-β-amino Acid Derivatives of Bestatin.

Published 2022 in J Med Chem, :

Reference #22022

Crook ZR; Girard EJ; Sevilla GP; Brusniak MY; Rupert PB; Friend DJ; Gewe MM; Clarke M; Lin I; Ruff R; Pakiam F; Phi TD; Bandaranayake A; Correnti CE; Mhyre AJ; Nairn NW; Strong RK; Olson JM

Ex silico engineering of cystine-dense peptides yielding a potent bispecific T cell engager.

Published 2022 in Sci Transl Med, 14: eabn0402

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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