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PDBsum entry 2b5t
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Ligand/metal interactions PDB id
2b5t
Ligand highlighted
GU3-GU2-GU6-GU1-
GU5-GU8-GU9-GU8-
GU9-GU8-GU9-GU8-
GU5-GU0-GU6-GU4
Ligands
NAG-FUC ×2
NAG 1(E) to FUC 2(E)
GU3-GU2-GU6-GU1-
GU5-GU8-GU9-GU8-
GU9-GU8-GU9-GU8-
GU5-GU0-GU6-GU4
GU3 1(G) to GU4 16(G)
NAG-NAG-BMA-MAN-
MAN-MAN-FUC
NAG 1(H) to FUC 7(H)
NAG-NAG
NAG 1(J) to NAG 2(J)
GOL ×12
GOL 1102(A)
GOL 1108(A)
GOL 1101(B)
GOL 1103(B)
GOL 1104(B)
GOL 1105(B)
GOL 1109(B)
GOL 1107(D)
GOL 1111(D)
GOL 1112(I)
SO4 ×6
SO4 2001(B)
SO4 2002(B)
SO4 2003(B)
SO4 2006(B)
SO4 2005(I)
NAG
NAG 801(I)
  
Ligand GU3-GU2-GU6-GU1-GU5-GU8-GU9-GU8-GU9-GU8-GU9-GU8-GU5-GU0-GU6-GU4

GU3 - Methyl 3-O-Methyl-2,6-Di-O-Sulfo-Alpha-D- Glucopyranoside [Methyl 3-O-Methyl-2,6-Di-O-Sulfo-Alpha-D-Glucoside; methyl 3-O-Methyl-2,6-Di-O-Sulfo-D-Glucoside; methyl 3-O-Methyl-2,6-Di-O-Sulfo-Glucoside] Formula: C8H16O12S2
GU2 - 2,3-Di-O-Methyl-Alpha-L-Idopyranuronic acid [2,3-Di-O-Methyl-Alpha-L-Iduronic acid; 2,3-Di-O-Methyl- L-Iduronic acid; 2,3-Di-O-Methyl-Iduronic acid] Formula: C8H14O7
GU6 - 2,3,6-Tri-O-Sulfo-Alpha-D-Glucopyranose [2,3,6-Tri-O-Sulfonato-Alpha-D-Glucopyranose; 2,3,6-Tri- O-Sulfo-Alpha-D-Glucose; 2,3,6-Tri-O-Sulfo-D-Glucose; 2,3,6-Tri-O-Sulfo-Glucose] Formula: C6H12O15S3
GU1 - 2,3-Di-O-Methyl-Beta-D-Glucopyranuronic acid [2,3-Di-O-Methyl-Beta-D-Glucuronic acid; 2,3-Di-O- Methyl-D-Glucuronic acid; 2,3-Di-O-Methyl-Glucuronic acid] Formula: C8H14O7
GU5 - 2,3-Di-O-Methyl-6-O-Sulfonato-Alpha-D-Glucopyranose [2,3-Di-O-Methyl-6-O-Sulfonato-Alpha-D-Glucose; 2,3-Di- O-Methyl-6-O-Sulfonato-D-Glucose; 2,3-Di-O-Methyl-6-O- Sulfonato-Glucose] Formula: C8H15O9S
GU8 - 2,3,6-Tri-O-Methyl-Beta-D-Glucopyranose [2,3,6-Tri-O-Methyl-Beta-D-Glucose; 2,3,6-Tri-O-Methyl- D-Glucose; 2,3,6-Tri-O-Methyl-Glucose] Formula: C9H18O6
GU9 - 2,3,6-Tri-O-Methyl-Alpha-D-Glucopyranose [2,3,6-Tri-O-Methyl-Alpha-D-Glucose; 2,3,6-Tri-O-Methyl- D-Glucose; 2,3,6-Tri-O-Methyl-Glucose] Formula: C9H18O6
GU0 - 2,3,6-Tri-O-Sulfonato-Beta-D-Glucopyranose [2,3,6-Tri-O-Sulfonato-Beta-D-Glucose; 2,3,6-Tri-O- Sulfonato-D-Glucose; 2,3,6-Tri-O-Sulfonato-Glucose] Formula: C6H9O15S33
GU4 - 2,3,4,6-Tetra-O-Sulfonato-Alpha-D-Glucopyranose [2,3,4,6-Tetra-O-Sulfonato-Alpha-D-Glucose; 2,3,4,6- Tetra-O-Sulfonato-D-Glucose; 2,3,4,6-Tetra-O- Sulfonato-Glucose] Formula: C6H12O18S4
Validation of ligand annotation
Per Residue Validation
Atoms Missing Incorrect Chiral Centres
Residue Dic. Struc. Link Subs. Atoms Rings Planar High C Other
GU3 1(G) 22 22 0 0 Complete Chiral checks - OK
GU2 2(G) 15 15 1 0 Complete Chiral checks - OK
GU6 3(G) 24 24 1 0 Complete Chiral checks - OK
GU1 4(G) 15 15 1 0 Complete Chiral checks - OK
GU5 5(G) 18 18 1 0 Complete Chiral checks - OK
GU8 6(G) 15 15 1 0 Complete Chiral checks - OK
GU9 7(G) 15 15 1 0 Complete Chiral checks - OK
GU8 8(G) 15 15 1 0 Complete Chiral checks - OK
GU9 9(G) 15 15 1 0 Complete Chiral checks - OK
GU8 10(G) 15 15 1 0 Complete Chiral checks - OK
GU9 11(G) 15 15 1 0 Complete Chiral checks - OK
GU8 12(G) 15 15 1 0 Complete Chiral checks - OK
GU5 13(G) 18 18 1 0 Complete Chiral checks - OK
GU0 14(G) 24 24 1 0 Complete Chiral checks - OK
GU6 15(G) 24 24 1 0 Complete Chiral checks - OK
GU4 16(G) 28 28 1 0 Complete Chiral checks - OK
Advanced Analysis
Residue Name Mismatches Count
GU3 1(G) - 0
GU2 2(G) - 0
GU6 3(G) - 0
GU1 4(G) - 0
GU5 5(G) - 0
GU8 6(G) - 0
GU9 7(G) - 0
GU8 8(G) - 0
GU9 9(G) - 0
GU8 10(G) - 0
GU9 11(G) - 0
GU8 12(G) - 0
GU5 13(G) O31: O32|O33: O31 2
GU0 14(G) - 0
GU6 15(G) O15: O13|O13: O14|O18: O17|O17: O18|O20: O19... 6
GU4 16(G) - 0
Additional Information
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  JSmol

LIGPLOT of interactions involving ligand GU3-GU2-GU6-GU1-GU5-GU8-GU9-GU8-GU9-GU8-GU9-GU8-GU5-GU0-GU6-GU4

JSmol




List of
interactions
 

GU3 1(G) to GU4 16(G)
  
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