Glycosciences.de - Glycosciences.DB entry 298

Format: CarbBank LINUCS GlycoCT_xml


       a-D-Manp-(1-2)-a-D-Manp-(1-6)+
                                    |
                               a-D-Manp-(1-6)+
                                    |        |
       a-D-Manp-(1-2)-a-D-Manp-(1-3)+   b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-Asn
                                             |
 a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+


<?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>
 <basetype id="7" anomer="a" superclass="hex" ringStart="1" ringEnd="5" name="a-dman-HEX-1:5">
 <stemtype id="1" type="dman" />
 </basetype>
 <basetype id="8" anomer="a" superclass="hex" ringStart="1" ringEnd="5" name="a-dman-HEX-1:5">
 <stemtype id="1" type="dman" />
 </basetype>
 <basetype id="9" anomer="a" superclass="hex" ringStart="1" ringEnd="5" name="a-dman-HEX-1:5">
 <stemtype id="1" type="dman" />
 </basetype>
 <basetype id="10" anomer="a" superclass="hex" ringStart="1" ringEnd="5" name="a-dman-HEX-1:5">
 <stemtype id="1" type="dman" />
 </basetype>
 <basetype id="11" anomer="a" superclass="hex" ringStart="1" ringEnd="5" name="a-dman-HEX-1:5">
 <stemtype id="1" type="dman" />
 </basetype>
 <basetype id="12" anomer="a" superclass="hex" ringStart="1" ringEnd="5" name="a-dman-HEX-1:5">
 <stemtype id="1" type="dman" />
 </basetype>
 <basetype id="13" 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>
 <connection id="6" parent="6" child="7">
 <linkage id="6" parentType="o" childType="d">
 <parent pos="2" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="7" parent="7" child="8">
 <linkage id="7" parentType="o" childType="d">
 <parent pos="2" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="8" parent="5" child="9">
 <linkage id="8" parentType="o" childType="d">
 <parent pos="6" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="9" parent="9" child="10">
 <linkage id="9" parentType="o" childType="d">
 <parent pos="3" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="10" parent="10" child="11">
 <linkage id="10" parentType="o" childType="d">
 <parent pos="2" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="11" parent="9" child="12">
 <linkage id="11" parentType="o" childType="d">
 <parent pos="6" />
 <child pos="1" />
 </linkage>
 </connection>
 <connection id="12" parent="12" child="13">
 <linkage id="12" parentType="o" childType="d">
 <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>

download coordinates

1 - 5 of 6 entries with matching glycan part

Structure entry #1927: Man-9 N-Glycan linked to Asn

a-D-Manp-(1-2)-a-D-Manp-(1-6)+ | a-D-Manp-(1-6)+ | | a-D-Manp-(1-2)-a-D-Manp-(1-3)+ b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-Asn-(1-2)-Phe | a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+

: 1

Taxons

Structure entry #2909: Man-9 N-glycan linked to dolichol diphosphate

a-D-Manp-(1-2)-a-D-Manp-(1-6)+ | a-D-Manp-(1-6)+ | | a-D-Manp-(1-2)-a-D-Manp-(1-3)+ b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-O)-dolichol-PP | a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+

: 4

Taxons

Structure entry #7773: Man-9 N-glycan linked to acetohydrazine

a-D-Manp-(1-2)-a-D-Manp-(1-6)+ | a-D-Manp-(1-6)+ | | a-D-Manp-(1-2)-a-D-Manp-(1-3)+ b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-O)-<acetohydrazine> | a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+

: 1

Taxons

Structure entry #12243: Lipid-linked Man-9 N-glycan

a-D-Manp-(1-2)-a-D-Manp-(1-6)+ | a-D-Manp-(1-6)+ | | a-D-Manp-(1-2)-a-D-Manp-(1-3)+ b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-O)-<Lipid> | a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+

: 1

Taxons

Structure entry #13776: Man-9 N-glycan linked to glycerophospholipid

a-D-Manp-(1-2)-a-D-Manp-(1-6)+ | a-D-Manp-(1-6)+ | | a-D-Manp-(1-2)-a-D-Manp-(1-3)+ b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-2)-ethanolamine-(1-O)-P-(O-3)+ | | a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+ Hexadecanoate-(1-2)-Glycerol | Hexadecanoate-(1-1)+

: 1

Taxons

N-glycan core (Show) (Search Database)

Man-9 N-glycan
Man-9
M9

N-Glycan
high-mannose

Chemical Formula:	C₇₄H₁₂₄N₄O₅₇	#C	#H	#O	#N
Molec. Weight:	1981	74	124	57	4
# Atoms:	259
# Residues:	12
# Heavy Atoms:	135

Superclasses:

Hex
Hex	9
HexNAc	2

Residues:

Residue	Count
A-D-MANP	8
ASN	1
B-D-GLCPNAC	2
B-D-MANP	1

MHz	500
Temperature	300
Solvent	D2O
Note	a)Assignments may have to be interchanged.
Residue	Linkage	Proton	PPM	JFrom	JTo	Hz	Note
b-D-GlcpNAc	4	H1	5.092			0
b-D-GlcpNAc	4	NAC	2.015			0
b-D-GlcpNAc	4,4	H1	4.610			0
b-D-GlcpNAc	4,4	NAC	2.067			0
b-D-Manp	4,4,4	H1	4.770			0
b-D-Manp	4,4,4	H2	4.228			0
a-D-Manp	6,4,4,4	H1	4.869			0
a-D-Manp	6,4,4,4	H2	4.156			0
a-D-Manp	6,6,4,4,4	H1	5.143			0
a-D-Manp	6,6,4,4,4	H2	4.023			0
a-D-Manp	2,6,6,4,4,4	H1	5.042			0
a-D-Manp	2,6,6,4,4,4	H2	4.066			0	a
a-D-Manp	3,6,4,4,4	H1	5.404			0
a-D-Manp	3,6,4,4,4	H2	4.109			0
a-D-Manp	2,3,6,4,4,4	H1	5.061			0
a-D-Manp	2,3,6,4,4,4	H2	4.073			0	a
a-D-Manp	3,4,4,4	H1	5.334			0
a-D-Manp	3,4,4,4	H2	4.098			0
a-D-Manp	2,3,4,4,4	H1	5.308			0
a-D-Manp	2,3,4,4,4	H2	4.109			0
a-D-Manp	2,2,3,4,4,4	H1	5.049			0
a-D-Manp	2,2,3,4,4,4	H2	4.073			0	a

1 - 5 of 19 PDB entries

PDB ID 7mxe: Ab1245 Fab in complex with BG505 SOSIP.664 and 8ANC195 Fab

Description:

Source: HOMO SAPIENS, Human immunodeficiency virus 1, Macaca mulatta

Experimental method: ELECTRON MICROSCOPY

Release date: 2021-10-27

Entry features 8 distinct glycan structures [55 instances].

PDB ID 6utk: Crystal structure of 438-B11 Fab in complex with an uncleaved prefusion optimized (UFO) soluble BG505 trimer and Fab 35O22 at 3.80 Angstrom

Description: 35O22 Fab Heavy Chain, 35O22 Fab Light Chain, B11 Fab Light Chain, Envelope glycoprotein gp120, Envelope glycoprotein gp41, B11 Fab Heavy chain

Source: Homo sapiens, Human immunodeficiency virus 1

Experimental method: X-RAY DIFFRACTION

Resolution: 3.8Å

Release date: 2020-09-23

Entry features 10 distinct glycan structures [23 instances].

PDB ID 6pzf: Crystal structure of human NA-63 Fab in complex with neuraminidase from A/Hunan/02650/2016(H7N9)

Description: Neuraminidase (E.C.3.2.1.18), NA-63 Fab light chain, NA-63 Fab heavy chain

Source: Influenza A virus (A/Hunan/02650/2016(H7N9), Homo sapiens

Experimental method: X-RAY DIFFRACTION

Resolution: 2.8Å

Release date: 2019-12-04

Entry features 3 distinct glycan structures [5 instances].

PDB ID 6q1z: Crystal structure of human 1G04 Fab in complex with influenza virus neuraminidase from A/Hunan/02650/2016 (H7N9)

Description: Neuraminidase (E.C.3.2.1.18), 1G04 Fab kappa light chain, 1G04 Fab IgG1 heavy chain

Source: Influenza A virus, Homo sapiens

Experimental method: X-RAY DIFFRACTION

Resolution: 3.446Å

Release date: 2019-10-23

Entry features 3 distinct glycan structures [6 instances].

PDB ID 6i2k: Structure of EV71 complexed with its receptor SCARB2

Description: Polyprotein, Lysosome membrane protein 2

Source: Enterovirus A71, Homo sapiens

Experimental method: ELECTRON MICROSCOPY

Release date: 2018-11-28

Entry features 6 distinct glycan structures [8 instances].

1 - 5 of 72 literature references

Reference #21822

Mabashi-Asazuma H; Jarvis DL

A new insect cell line engineered to produce recombinant glycoproteins with cleavable N-glycans.

Published 2022 in J Biol Chem, 298: 101454

Reference contains 4 structures

Reference #21693

Nguyen K; Chakraborty S; Mansbach RA; Korber B; Gnanakaran S

Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2.

Published 2021 in Viruses, 13:

Reference contains 2 structures

Reference #21760

Matthies I; Abrahams JL; Jensen P; Oliveira T; Kolarich D; Larsen MR

N-Glycosylation in isolated rat nerve terminals.

Published 2021 in Mol Omics, 17: 517-532

Reference contains 26 structures

Reference #21676

Messina A; Palmigiano A; Esposito F; Fiumara A; Bordugo A; Barone R; Sturiale L; Jaeken J; Garozzo D

HILIC-UPLC-MS for high throughput and isomeric N-glycan separation and characterization in Congenital Disorders Glycosylation and human diseases.

Published 2021 in Glycoconj J, 38: 201-211

Reference contains 19 structures

Reference #21819

Alam SMD; Tsukamoto Y; Ogawa M; Senoo Y; Ikeda K; Tashima Y; Takeuchi H; Okajima T

N-Glycans on EGF domain-specific O-GlcNAc transferase (EOGT) facilitate EOGT maturation and peripheral endoplasmic reticulum localization.

Published 2020 in J Biol Chem, 295: 8560-8574

Reference contains 3 structures

1 - 5 of 8 literature references from PDB entries

Reference #21310

Zhu X; Turner HL; Lang S; McBride R; Bangaru S; Gilchuk IM; Yu W; Paulson JC; Crowe JE; Ward AB; Wilson IA

Structural Basis of Protection against H7N9 Influenza Virus by Human Anti-N9 Neuraminidase Antibodies.

Published 2019 in Cell Host Microbe, :

Reference #20231

Zhu Q; McLellan JS; Kallewaard NL; Ulbrandt ND; Palaszynski S; Zhang J; Moldt B; Khan A; Svabek C; McAuliffe JM; Wrapp D; Patel NK; Cook KE; Richter BWM; Ryan PC; Yuan AQ; Suzich JA

A highly potent extended half-life antibody as a potential RSV vaccine surrogate for all infants.

Published 2017 in Sci Transl Med, 9:

Reference #19593

Kong L; He L; de Val N; Vora N; Morris CD; Azadnia P; Sok D; Zhou B; Burton DR; Ward AB; Wilson IA; Zhu J

Uncleaved prefusion-optimized gp140 trimers derived from analysis of HIV-1 envelope metastability.

Published 2016 in Nat Commun, 7: 12040

Reference #20034

Jardine JG; Sok D; Julien JP; Briney B; Sarkar A; Liang CH; Scherer EA; Henry Dunand CJ; Adachi Y; Diwanji D; Hsueh J; Jones M; Kalyuzhniy O; Kubitz M; Spencer S; Pauthner M; Saye-Francisco KL; Sesterhenn F; Wilson PC; Galloway DM; Stanfield RL; Wilson I

Minimally Mutated HIV-1 Broadly Neutralizing Antibodies to Guide Reductionist Vaccine Design.

Published 2016 in PLoS Pathog., 12: e1005815

Reference #19475

Agirre J; Ariza A; Offen WA; Turkenburg JP; Roberts SM; McNicholas S; Harris PV; McBrayer B; Dohnalek J; Cowtan KD; Davies GJ; Wilson KS

Three-dimensional structures of two heavily N-glycosylated Aspergillus sp. family GH3 β-D-glucosidases.

Published 2016 in Acta Crystallogr D Struct Biol, 72: 254-65

NCBI Taxonomy ID	Scientific Name
85823	Blattaria
9913	Bos taurus
10141	Cavia porcellus
93934	Coturnix japonica
3847	Glycine max
9606	Homo sapiens
12721	Human immunodeficiency virus
7130	Manduca sexta
3885	Phaseolus vulgaris
10114	Rattus
6855	Scorpiones

Consortium for Functional Glycomics (CFG):

Glycosciences.DB structure entry #298: Man-9 N-glycan linked to Asn

1 - 5 of 6 entries with matching glycan part

1 - 5 of 19 PDB entries

1 - 5 of 72 literature references

1 - 5 of 8 literature references from PDB entries

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