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Glycosciences.DB structure entry #551: N-Glycan fragment GlcNAc2Man1

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Format: CarbBank LINUCS GlycoCT_xml


 b-D-Manp-(1-4)-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" />
 <basetype id="5" anomer="b" superclass="hex" ringStart="1" ringEnd="5" name="b-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>
 </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: 8

1 - 5 of 8 entries with matching glycan part

Structure entry #3409:

b-D-Manp-(1-4)-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

Structure entry #3821:

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

no NMR spectra

literature references

GlycoMaps

Structure entry #5704:

b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-7)-<7-amino-4-methyl-2h-1-benzopyran-2-one>

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #13373:

b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)+ | Asn-(1-2)-Tyr-(1-2)-Thr | octanoate-(1-2)+

no NMR spectra

literature references

no GlycoMaps

Structure entry #13729:

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

no NMR spectra

literature references

no GlycoMaps

General Structure Data

Chemical Formula:	C₂₆H₄₄N₄O₁₇		#C	#H	#O	#N
Molec. Weight:	684		26	44	17	4
# Atoms:	91
# Residues:	4
# Heavy Atoms:	47

Superclasses:

Hex
Hex	1
HexNAc	2

Residues:

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

PDB references: 1422

1 - 5 of 1422 PDB entries

PDB ID 7xwa: Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.4/5 variant spike protein in complex with its receptor ACE2

Description:

Source: Homo sapiens, Severe acute respiratory syndrome coronavirus 2

Experimental method: X-RAY DIFFRACTION

Resolution: 3.36Å

Release date: 2022-09-28

Entry features 5 distinct glycan structures [11 instances].

PDB ID 7qng: Structure of a MHC I-Tapasin-ERp57 complex

Description:

Source: Homo sapiens, Mus musculus

Experimental method: X-RAY DIFFRACTION

Resolution: 2.7Å

Release date: 2022-09-28

Entry features 1 distinct glycan structures [1 instances].

PDB ID 7sch: Cryo-EM structure of the human Exostosin-1 and Exostosin-2 heterodimer

Description:

Source: Homo sapiens

Experimental method: ELECTRON MICROSCOPY

Release date: 2022-09-28

Entry features 1 distinct glycan structures [1 instances].

PDB ID 7scj: Cryo-EM structure of the human Exostosin-1 and Exostosin-2 heterodimer in complex with a 4-sugar oligosaccharide acceptor analog

Description:

Source: Homo sapiens

Experimental method: ELECTRON MICROSCOPY

Release date: 2022-09-28

Entry features 3 distinct glycan structures [3 instances].

PDB ID 7sck: Cryo-EM structure of the human Exostosin-1 and Exostosin-2 heterodimer in complex with a 7-sugar oligosaccharide acceptor analog

Description:

Source: Homo sapiens

Experimental method: ELECTRON MICROSCOPY

Release date: 2022-09-28

Entry features 3 distinct glycan structures [3 instances].

Literature references: 12

1 - 5 of 12 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

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 #9863

Trimble RB; Tarentino AL

Identification of distinct endoglycosidase (endo) activities in Flavobacterium meningosepticum: endo F1, endo F2, and endo F3. Endo F1 and endo H hydrolyze only high mannose and hybrid glycans

Published 1991 in J Biol Chem, 266: 1646-1651

Reference contains 19 structures

Guenther W; Kunz H

Synthesis of a .beta.-mannosyl-chitobiosyl-asparagine conjugate- a central core region unit of the N-glycoproteins

Published 1990 in Angew Chem Int Ed, 29: 1050-1051

Reference contains 1 structure

Maley F; Trimble RB; Tarentino AL; Plummer TH

Characterization of glycoproteins and their associated oligosaccharides through the use of endoglycosidases

Published 1989 in Anal Biochem, 180: 195-204

Reference contains 16 structures

Further literature references from PDB entries: 598

1 - 5 of 598 literature references from PDB entries

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 #22422

Wang A; Zhou F; Liu C; Gao D; Qi R; Yin Y; Liu S; Gao Y; Fu L; Xia Y; Xu Y; Wang C; Liu Z

Structure of infective Getah virus at 2.8 Å resolution determined by cryo-electron microscopy.

Published 2022 in Cell Discov, 8: 12

Reference #22305

Feng B; Chen Z; Sun J; Xu T; Wang Q; Yi H; Niu X; Zhu J; Fan M; Hou R; Shao Y; Huang S; Li C; Hu P; Zheng P; He P; Luo J; Yan Q; Xiong X; Liu J; Zhao J; Chen L

A Class of Shark-Derived Single-Domain Antibodies can Broadly Neutralize SARS-Related Coronaviruses and the Structural Basis of Neutralization and Omicron Escape.

Published 2022 in Small Methods, : e2200387

Reference #21941

Cao L; Coventry B; Goreshnik I; Huang B; Park JS; Jude KM; Marković I; Kadam RU; Verschueren KHG; Verstraete K; Walsh STR; Bennett N; Phal A; Yang A; Kozodoy L; DeWitt M; Picton L; Miller L; Strauch EM; DeBouver ND; Pires A; Bera AK; Halabiya S; Hammers

Design of protein binding proteins from target structure alone.

Published 2022 in Nature, :

Reference #21982

Hodder AN; Christensen J; Scally S; Triglia T; Ngo A; Birkinshaw RW; Bailey B; Favuzza P; Dietrich MH; Tham WH; Czabotar PE; Lowes K; Guo Z; Murgolo N; Lera Ruiz M; McCauley JA; Sleebs BE; Olsen D; Cowman AF

Basis for drug selectivity of plasmepsin IX and X inhibition in Plasmodium falciparum and vivax.

Published 2022 in Structure, :

NCBI Taxonomy ID	Scientific Name
9913	Bos taurus
9031	Gallus gallus
9606	Homo sapiens

Consortium for Functional Glycomics (CFG):

carbNlink_20508_D000

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