SMTL ID : 3zw2.1

Structure of the lectin Bambl from Burkholderia ambifaria in complex with blood group H type 1 tetrasaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

4 x NAG- GAL- FUC: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-FUC.1: 12 residues within 4Å: Chain A: S.13, R.15, E.26, D.30, Y.35, G.37, A.38, F.39, I.59, W.74, G.76, W.79 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.59 Hydrogen bonds: A:R.15, A:E.26, A:A.38, A:F.39, A:S.13, A:S.13, A:Y.35, A:Y.35 Water bridges: A:V.57, A:W.74 NAG-GAL-FUC.3: 12 residues within 4Å: Chain B: W.8, R.15, E.26, D.30, Y.35, G.37, A.38, F.39, V.57, I.59, W.74, W.79 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.59, B:V.57 Hydrogen bonds: B:R.15, B:E.26, B:A.38, B:F.39, B:R.15, B:D.30, B:Y.35, B:Y.35 Water bridges: B:W.8, B:S.13, B:S.13 NAG-GAL-FUC.4: 12 residues within 4Å: Chain B: W.51, H.58, R.60, E.71, D.75, G.82, A.83, Y.84 Chain C: P.12, I.14, Y.29, W.34 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:W.51, C:I.14, C:Y.29 Hydrogen bonds: B:R.60, B:E.71, B:A.83, B:Y.84, B:H.58 Water bridges: B:R.60 NAG-GAL-FUC.6: 14 residues within 4Å: Chain A: T.11, P.12, I.14, Y.29, W.34 Chain C: W.51, H.58, R.60, E.71, D.75, D.77, G.82, A.83, Y.84 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:W.51, A:I.14, A:Y.29 Hydrogen bonds: C:R.60, C:E.71, C:A.83, C:Y.84, C:R.60, C:D.77 Salt bridges: C:H.58

1 x GAL- FUC: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose(Non-covalent)

GAL-FUC.2: 10 residues within 4Å: Chain A: W.51, R.60, E.71, G.82, A.83, Y.84 Chain B: P.12, I.14, Y.29, W.34 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.51, B:I.14, B:Y.29 Hydrogen bonds: A:R.60, A:E.71, A:A.83, A:Y.84, B:Y.29, B:Y.29 Water bridges: A:A.83

1 x GLA- NAG- GAL- FUC: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-galactopyranose

GLA-NAG-GAL-FUC.5: 15 residues within 4Å: Chain C: W.8, S.13, R.15, E.26, D.30, Y.35, G.37, A.38, F.39, S.55, V.57, I.59, W.74, G.76, W.79 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.57, C:I.59 Hydrogen bonds: C:R.15, C:E.26, C:A.38, C:F.39, C:S.13, C:S.13, C:Y.35, C:S.55 Water bridges: C:V.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Audfray, A. et al., Fucose-Binding Lectin from Opportunistic Pathogen Burkholderia Ambifaria Binds to Both Plant and Human Oligosaccharidic Epitopes. J.Biol.Chem. (2012)

Release Date

2011-11-16

Peptides

BAMBL LECTIN: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

BAMBL LECTIN

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