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Glycosciences.DB structure entry #139: Raffinose

Format: CarbBank LINUCS GlycoCT_condensed GlycoCT_xml


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


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>

download coordinates

Raffinose

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General Structure Data

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

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Composition

Superclasses:

Hex
Hex	3

Residues:

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

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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

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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