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Glycosciences.DB structure entry #1516:

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Format: CarbBank LINUCS GlycoCT_xml


 a-D-Manp-(1-3)-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>
 <basetype id="6" anomer="a" superclass="hex" ringStart="1" ringEnd="5" name="a-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>
 <connection id="5" parent="5" child="6">
 <linkage id="5" parentType="o" childType="d">
 <parent pos="3" />
 <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: 4

1 - 4 of 4 entries with matching glycan part

Structure entry #3410:

a-D-Manp-(1-3)-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 #5705:

a-D-Manp-(1-3)-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 #23248:

a-D-Manp-(1-3/6)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #23412:

a-D-Manp-(1-3)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc

no NMR spectra

literature references

no GlycoMaps

Taxons

General Structure Data

Chemical Formula:	C₃₂H₅₄N₄O₂₂		#C	#H	#O	#N
Molec. Weight:	846		32	54	22	4
# Atoms:	112
# Residues:	5
# Heavy Atoms:	58

Superclasses:

Hex
Hex	2
HexNAc	2

Residues:

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

PDB references: 500

1 - 5 of 500 PDB entries

PDB ID 7qti: SARS-CoV-2 S Omicron Spike B.1.1.529 - 3-P2G3 and 1-P5C3 Fabs (Global)

Description:

Source: HOMO SAPIENS, Severe acute respiratory syndrome coronavirus 2

Experimental method: ELECTRON MICROSCOPY

Release date: 2022-08-03

Entry features 4 distinct glycan structures [43 instances].

PDB ID 7p57: VSG2 mutant structure lacking the calcium binding pocket

Description:

Source: Trypanosoma brucei brucei

Experimental method: X-RAY DIFFRACTION

Resolution: 1.961Å

Release date: 2022-07-27

Entry features 1 distinct glycan structures [1 instances].

PDB ID 7q4e: Local refinement structure of a single N-domain of full-length, dimeric, soluble somatic angiotensin I-converting enzyme

Description:

Source: Homo sapiens

Experimental method: ELECTRON MICROSCOPY

Release date: 2022-07-20

Entry features 6 distinct glycan structures [8 instances].

PDB ID 7q4d: Local refinement structure of the two interacting N-domains of full-length, dimeric, soluble somatic angiotensin I-converting enzyme

Description:

Source: Homo sapiens

Experimental method: ELECTRON MICROSCOPY

Release date: 2022-07-20

Entry features 6 distinct glycan structures [16 instances].

PDB ID 8cyb: SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-8

Description:

Source: Severe acute respiratory syndrome coronavirus 2, Lama glama

Experimental method: ELECTRON MICROSCOPY

Release date: 2022-07-06

Entry features 8 distinct glycan structures [54 instances].

Literature references: 2

1 - 2 of 2 literature references

Reference #9960

Aleshin A; Golubev A; Firsov LM; Honzatko RB

Crystal structure of glucoamylase from Aspergillus awamori var. X100 to 2.2-A resolution

Published 1992 in J Biol Chem, 267: 19291-19298

Reference contains 2 structures

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: 226

1 - 5 of 226 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 #22427

Fenwick C; Turelli P; Ni D; Perez L; Lau K; Herate C; Marlin R; Lana E; Pellaton C; Raclot C; Esteves-Leuenberger L; Campos J; Farina A; Fiscalini F; Dereuddre-Bosquet N; Relouzat F; Abdelnabi R; Foo CS; Neyts J; Leyssen P; Lévy Y; Pojer F; Stahlberg H;

Patient-derived monoclonal antibody neutralizes SARS-CoV-2 Omicron variants and confers full protection in monkeys.

Published 2022 in Nat Microbiol, :

Reference #22054

Xiang Y; Huang W; Liu H; Sang Z; Nambulli S; Tubiana J; Williams KL; Duprex WP; Schneidman-Duhovny D; Wilson IA; Taylor DJ; Shi Y

Superimmunity by pan-sarbecovirus nanobodies.

Published 2022 in Cell Rep, 39: 111004

Reference #21443

Jette CA; Barnes CO; Kirk SM; Melillo B; Smith AB; Bjorkman PJ

Cryo-EM structures of HIV-1 trimer bound to CD4-mimetics BNM-III-170 and M48U1 adopt a CD4-bound open conformation.

Published 2021 in Nat Commun, 12: 1950

Reference #21533

Kondo T; Kichijo M; Maruta A; Nakaya M; Takenaka S; Arakawa T; Fushinobu S; Sakamoto T

Structural and functional analysis of gum arabic l-rhamnose-α-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family.

Published 2021 in J Biol Chem, 297: 101001

Reference contains 9 structures

Consortium for Functional Glycomics (CFG):

carbNlink_20727_D000

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