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Glycosciences.DB structure entry #298: 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
|
a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+
[][ASN]{[(4+1)][B-D-GLCPNAC]{[(4+1)][B-D-GLCPNAC]{[(4+1)][B-D-MANP]{[(3+1)][A-D-MANP]{[(2+1)][A-D-MANP]{[(2+1)][A-D-MANP]{}}}[(6+1)][A-D-MANP]{[(3+1)][A-D-MANP]{[(2+1)][A-D-MANP]{}}[(6+1)][A-D-MANP]{[(2+1)][A-D-MANP]{}}}}}}}
<?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>

1 - 5 of 6 entries with matching glycan part

a-D-Manp-(1-2)-a-D-Manp-(1-6)+
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a-D-Manp-(1-6)+
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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
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a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+
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Taxons |

a-D-Manp-(1-2)-a-D-Manp-(1-6)+
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a-D-Manp-(1-6)+
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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
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a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+
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Taxons |

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>
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a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+
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Taxons |

a-D-Manp-(1-2)-a-D-Manp-(1-6)+
|
a-D-Manp-(1-6)+
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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>
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a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+
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Taxons |

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)+
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a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+ Hexadecanoate-(1-2)-Glycerol
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Hexadecanoate-(1-1)+
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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:
|
Residues:
|
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 18 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 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].

PDB ID 6cbp:
Crystal structure of the single chain variable fragment of the DH270.6 bnAb in complex with the Man9-V3 glycopeptide
Description: Man9-V3 glycopeptide,DH270.6 single chain variable fragment
Source: Homo sapiens
Experimental method: X-RAY DIFFRACTION
Resolution: 2.17Å
Release date: 2018-02-21
Entry features 2 distinct glycan structures [2 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 #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 #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 #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):
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