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Glycosciences.DB structure entry #139: Raffinose
a-D-Galp-(1-6)-a-D-Glcp-(1-2)-b-D-Fruf
[][B-D-FRUF]{[(2+1)][A-D-GLCP]{[(6+1)][A-D-GALP]{}}}
RES
1b:b-dara-HEX-2:5|2:keto
2b:a-dglc-HEX-1:5
3b:a-dgal-HEX-1:5
LIN
1:1o(2+1)2d
2:2o(6+1)3d
<?xml version="1.0" encoding="UTF-8"?>
<sugar version="1.0">
<residues>
<basetype id="1" anomer="b" superclass="hex" ringStart="2" ringEnd="5" name="b-dara-HEX-2:5|2:keto">
<stemtype id="1" type="dara" />
<modification type="keto" pos_one="2" />
</basetype>
<basetype id="2" anomer="a" superclass="hex" ringStart="1" ringEnd="5" name="a-dglc-HEX-1:5">
<stemtype id="1" type="dglc" />
</basetype>
<basetype id="3" anomer="a" superclass="hex" ringStart="1" ringEnd="5" name="a-dgal-HEX-1:5">
<stemtype id="1" type="dgal" />
</basetype>
</residues>
<linkages>
<connection id="1" parent="1" child="2">
<linkage id="1" parentType="o" childType="d">
<parent pos="2" />
<child pos="1" />
</linkage>
</connection>
<connection id="2" parent="2" child="3">
<linkage id="2" parentType="o" childType="d">
<parent pos="6" />
<child pos="1" />
</linkage>
</connection>
</linkages>
</sugar>
3D Structure Model- Raffinose
| Chemical Formula: | C18H32O16 | #C | #H | #O | |
| Molec. Weight: | 504 | 18 | 32 | 16 | |
| # Atoms: | 66 | ||||
| # Residues: | 3 | ||||
| # Heavy Atoms: | 34 | ||||
Superclasses:
|
Residues:
|
||||||||||||
NMR Carbon Chemical Shift Info| MHz | 0 | ||||||
| Temperature | 0 | ||||||
| Solvent | D2O | ||||||
| Residue | Linkage | Carbon | PPM | JFrom | JTo | Hz | Note |
| b-D-Fruf | C1 | 62.20 | 0 | ||||
| b-D-Fruf | C2 | 104.60 | 0 | ||||
| b-D-Fruf | C3 | 77.20 | 0 | ||||
| b-D-Fruf | C4 | 74.80 | 0 | ||||
| b-D-Fruf | C5 | 82.20 | 0 | ||||
| b-D-Fruf | C6 | 63.30 | 0 | ||||
| a-D-Glcp | 2 | C1 | 92.90 | 0 | |||
| a-D-Glcp | 2 | C2 | 71.80 | 0 | |||
| a-D-Glcp | 2 | C3 | 73.50 | 0 | |||
| a-D-Glcp | 2 | C4 | 70.30 | 0 | |||
| a-D-Glcp | 2 | C5 | 72.20 | 0 | |||
| a-D-Glcp | 2 | C6 | 66.70 | 0 | |||
| a-D-Galp | 6,2 | C1 | 99.30 | 0 | |||
| a-D-Galp | 6,2 | C2 | 69.30 | 0 | |||
| a-D-Galp | 6,2 | C3 | 70.30 | 0 | |||
| a-D-Galp | 6,2 | C4 | 70.00 | 0 | |||
| a-D-Galp | 6,2 | C5 | 71.80 | 0 | |||
| a-D-Galp | 6,2 | C6 | 61.90 | 0 | |||
PDB references: 121 - 5 of 12 PDB entries
PDB ID 6phx:
SpAga D472N structure in complex with raffinose
Description: Alpha-galactosidase (E.C.3.2.1.22)
Source: Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
Experimental method: X-RAY DIFFRACTION
Resolution: 2Å
Release date: 2019-10-02
Entry features 1 distinct glycan structures [1 instances].
PDB ID 6pql:
SBP RafE in complex with raffinose
Description: ABC transporter sugar-binding protein
Source: Streptococcus pneumoniae TIGR4
Experimental method: X-RAY DIFFRACTION
Resolution: 2.65Å
Release date: 2019-10-02
Entry features 1 distinct glycan structures [4 instances].
PDB ID 6epy:
Structure of the PBP MelB (Atu4661) in complex with raffinose from A.fabrum C58
Description: Periplasmic alpha-galactoside-binding protein
Source: Rhizobium radiobacter
Experimental method: X-RAY DIFFRACTION
Resolution: 2.04Å
Release date: 2018-04-11
Entry features 1 distinct glycan structures [4 instances].
PDB ID 4zs9:
Raffinose and panose binding protein from Bifidobacterium animalis subsp. lactis Bl-04, bound with raffinose
Description: Sugar binding protein of ABC transporter system
Source: Bifidobacterium animalis subsp. lactis Bl-04
Experimental method: X-RAY DIFFRACTION
Resolution: 1.37Å
Release date: 2016-06-29
Entry features 1 distinct glycan structures [2 instances].
PDB ID 4zza:
Raffinose and panose binding protein from Bifidobacterium animalis subsp. lactis Bl-04, bound with raffinose, selenomethionine derivative
Description: Sugar binding protein of ABC transporter system
Source: Bifidobacterium animalis subsp. lactis Bl-04
Experimental method: X-RAY DIFFRACTION
Resolution: 2.02Å
Release date: 2016-06-29
Entry features 1 distinct glycan structures [2 instances].
Literature references: 1031 - 5 of 103 literature references
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 #21137
Beshr G; Sikandar A; Jemiller EM; Klymiuk N; Hauck D; Wagner S; Wolf E; Koehnke J; Titz A
Photorhabdus luminescens lectin A (PllA): A new probe for detecting α-galactoside-terminating glycoconjugates.
Published 2017 in J. Biol. Chem., 292: 19935-19951
Reference contains 29 structures
Reference #2777
Kuriyama KI; Tsuchiya KY; Murui T
Some properties of transglycosylation activity of sesame .beta.-glucosidase
Published 1995 in Biosci Biotechnol Biochem, 59: 1142-1143
Reference contains 6 structures
Reference #6210
Somiari RI; Balogh E
Properties of an extracellular glycosidase of Aspergillus niger suitable for removal of oligosaccharides from cowpea meal
Published 1995 in Enzyme Microb Technol, 17: 311-316
Reference contains 3 structures
Reference #1433
Rodriguez J; Perez JA; Ruiz T; Rodriguez L
Characterization of the invertase from Pichia anomala
Published 1995 in Biochem J, 306: 235-239
Reference contains 1 structure
1 - 5 of 5 literature references from PDB entries
Reference #20451
Meyer T; Vigouroux A; Aumont-Niçaise M; Comte G; Vial L; Lavire C; Morera S
The plant defense signal galactinol is specifically used as a nutrient by the bacterial pathogen Agrobacterium fabrum.
Published 2018 in J. Biol. Chem., :
Reference #18297
Merceron R; Foucault M; Haser R; Mattes R; Watzlawick H; Gouet P
The molecular mechanism of thermostable α-galactosidases AgaA and AgaB explained by x-ray crystallography and mutational studies.
Published 2012 in J. Biol. Chem., 287: 39642-52
Reference #17754
Hatakeyama T; Kamiya T; Kusunoki M; Nakamura-Tsuruta S; Hirabayashi J; Goda S; Unno H
Galactose recognition by a tetrameric C-type lectin, CEL-IV, containing the EPN carbohydrate recognition motif.
Published 2011 in J. Biol. Chem., 286: 10305-15
Reference #17587
Fernández-Leiro R; Pereira-Rodríguez A; Cerdán ME; Becerra M; Sanz-Aparicio J
Structural analysis of Saccharomyces cerevisiae alpha-galactosidase and its complexes with natural substrates reveals new insights into substrate specificity of GH27 glycosidases.
Published 2010 in J. Biol. Chem., 285: 28020-33
Reference #17554
Chuankhayan P; Hsieh CY; Huang YC; Hsieh YY; Guan HH; Hsieh YC; Tien YC; Chen CD; Chiang CM; Chen CJ
Crystal structures of Aspergillus japonicus fructosyltransferase complex with donor/acceptor substrates reveal complete subsites in the active site for catalysis.
Published 2010 in J. Biol. Chem., 285: 23251-64
| NCBI Taxonomy ID | Scientific Name |
| 4501 | Bromus |
| 3650 | Cucurbitaceae |
| 3847 | Glycine max |
| 3864 | Lens culinaris |
| 4520 | Lolium |
| 3333 | Picea rubens |
| 3917 | Vigna unguiculata |
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