SMTL ID : 3zw1.2 (1 other biounit)

Structure of Bambl lectine in complex with lewix x antigen

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

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

GAL-NAG-FUC-GAL.1: 15 residues within 4Å: Chain A: W.51, R.60, E.71, D.75, T.80, R.81, G.82, A.83, Y.84 Chain B: T.11, P.12, I.14, Y.29, W.34 Ligands: GLA.3 2 PLIP interactions: 1 interactions with chain A, 1 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:T.11, B:Y.29, B:Y.29, B:Y.29 Water bridges: A:G.82, A:H.58 GAL-NAG-FUC-GAL.4: 15 residues within 4Å: Chain B: W.51, R.60, E.71, D.75, T.80, R.81, G.82, A.83, Y.84 Chain C: T.11, P.12, I.14, Y.29, W.34 Ligands: GLA.6 3 PLIP interactions: 1 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, C:T.11, C:Y.29 Water bridges: B:G.82, B:H.58, C:Y.29, C:Y.29 GAL-NAG-FUC-GAL.7: 15 residues within 4Å: Chain A: T.11, P.12, I.14, Y.29, W.34 Chain C: W.51, R.60, E.71, D.75, T.80, R.81, G.82, A.83, Y.84 Ligands: GLA.9 3 PLIP interactions: 1 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, A:T.11, A:Y.29 Water bridges: C:G.82, C:H.58, A:Y.29, A:Y.29

3 x NAG- FUC: alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-FUC.2: 11 residues within 4Å: Chain A: R.15, E.26, C.28, D.30, Y.35, G.37, A.38, F.39, I.59, W.74, W.79 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.59 Hydrogen bonds: A:R.15, A:E.26, A:A.38, A:F.39, A:R.15 Water bridges: A:T.36, A:Y.35, A:Y.35 NAG-FUC.5: 11 residues within 4Å: Chain B: R.15, E.26, C.28, D.30, Y.35, G.37, A.38, F.39, I.59, W.74, W.79 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.59 Hydrogen bonds: B:R.15, B:E.26, B:Y.35, B:A.38, B:F.39, B:R.15 Water bridges: B:T.36, B:D.30, B:D.30 NAG-FUC.8: 11 residues within 4Å: Chain C: R.15, E.26, C.28, D.30, Y.35, G.37, A.38, F.39, I.59, W.74, W.79 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.59 Hydrogen bonds: C:R.15, C:E.26, C:Y.35, C:A.38, C:F.39, C:R.15 Water bridges: C:T.36

3 x GLA: alpha-D-galactopyranose(Non-functional Binders)

GLA.3: 2 residues within 4Å: Ligands: GAL-NAG-FUC-GAL.1, GAL-NAG-FUC-GAL.1 No protein-ligand interaction detected (PLIP) GLA.6: 2 residues within 4Å: Ligands: GAL-NAG-FUC-GAL.4, GAL-NAG-FUC-GAL.4 No protein-ligand interaction detected (PLIP) GLA.9: 2 residues within 4Å: Ligands: GAL-NAG-FUC-GAL.7, GAL-NAG-FUC-GAL.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Topin, J. et al., Deciphering the Glycan Preference of Bacterial Lectins by Glycan Array and Molecular Docking with Validation by Microcalorimetry and Crystallography. Plos One (2013)

Release Date

2011-11-16

Peptides

BAMBL LECTIN: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

BAMBL LECTIN

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