Glycosciences.de - Glycosciences.DB entry 139

Glycosciences.DB structure entry #139: Raffinose

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a-D-Galp-(1-6)-a-D-Glcp-(1-2)-b-D-Fruf

3D Structure Model

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Raffinose

General Structure Data

Chemical Formula:	C₁₈H₃₂O₁₆		#C	#H	#O
Molec. Weight:	504		18	32	16
# Atoms:	66
# Residues:	3
# Heavy Atoms:	34

Superclasses:

Hex
Hex	3

Residues:

Residue	Count
A-D-GALP	1
A-D-GLCP	1
B-D-FRUF	1

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: 10

1 - 5 of 10 PDB entries

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].

PDB ID 4fnt: Crystal structure of GH36 alpha-galactosidase AgaA A355E D548N from Geobacillus stearothermophilus in complex with raffinose

Description: Alpha-galactosidase AgaA (E.C.3.2.1.22)

Source: Geobacillus stearothermophilus

Experimental method: X-RAY DIFFRACTION

Resolution: 2.6Å

Release date: 2012-10-03

Entry features 1 distinct glycan structures [3 instances].

PDB ID 3alu: Crystal structure of CEL-IV complexed with Raffinose

Description: Lectin CEL-IV, C-type

Source: Cucumaria echinata

Experimental method: X-RAY DIFFRACTION

Resolution: 1.65Å

Release date: 2011-01-19

Entry features 1 distinct glycan structures [4 instances].

Literature references: 101

1 - 5 of 101 literature references

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

Reference #2757

Muramatsu M; Nakakuki T

Enzymatic synthesis of novel fructosyl and oligofructosyl trehaloses by Aspergillus sydowi .beta.-fructofuranosidase

Published 1995 in Biosci Biotechnol Biochem, 59: 208-212

Reference contains 7 structures

Reference #7307

Monsan P; Paul F

Enzymatic synthesis of oligosaccharides

Published 1995 in FEMS Microbiol Rev, 16: 187-192

Reference contains 15 structures

Further literature references from PDB entries: 5

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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