SMTL ID : 6zzw.1

Structure of the N terminal domain of Bc2L-C lectin (1-131) in complex with Globo H (H-type 3) and CAS No 912569-62-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

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

GAL-GLA-NGA-GAL-FUC.1: 10 residues within 4Å: Chain A: Y.51, E.84, S.85, T.86, G.87, R.88 Chain B: F.57, T.77, R.114 Ligands: QT5.4 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.51, B:F.57 Hydrogen bonds: A:R.88, B:T.77, B:T.77, B:R.114, B:R.114, B:R.114 Water bridges: A:S.85, B:Y.61, A:T.86, A:T.86 GAL-GLA-NGA-GAL-FUC.3: 13 residues within 4Å: Chain A: N.56, F.57, Y.61, T.77, V.113, R.114 Chain C: Y.51, E.84, S.85, T.86, G.87, R.88 Ligands: QT5.7 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:Y.51, A:F.57 Hydrogen bonds: C:R.88, A:T.77, A:T.77, A:R.114, A:R.114, A:Y.61, A:R.114, C:S.85 Water bridges: C:S.85, C:R.88, A:Y.61, A:T.77, A:R.114, C:R.88

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

GLA-NGA-GAL-FUC.2: 10 residues within 4Å: Chain B: Y.51, E.84, S.85, T.86, G.87, R.88 Chain C: F.57, T.77, R.114 Ligands: QT5.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.51, C:F.57 Hydrogen bonds: B:R.88, C:T.77, C:T.77, C:R.114, C:R.114, C:R.114 Water bridges: B:S.85, C:Y.61, B:R.88, B:R.88, B:T.86, B:R.88

3 x QT5: [3-(2-methylimidazol-1-yl)phenyl]methanamine(Non-covalent)

QT5.4: 6 residues within 4Å: Chain A: R.88, D.121, S.122 Chain B: Y.61, D.73 Ligands: GAL-GLA-NGA-GAL-FUC.1 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.88, B:D.73 Hydrophobic interactions: B:Y.61 QT5.6: 6 residues within 4Å: Chain B: R.88, D.121, S.122 Chain C: Y.61, D.73 Ligands: GLA-NGA-GAL-FUC.2 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Y.61 Hydrogen bonds: C:D.73, B:R.88 QT5.7: 6 residues within 4Å: Chain A: Y.61, D.73 Chain C: R.88, D.121, S.122 Ligands: GAL-GLA-NGA-GAL-FUC.3 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.88, A:D.73 Hydrophobic interactions: A:Y.61

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 2 residues within 4Å: Chain A: Q.68, G.69 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lal, K. et al., Prediction and Validation of a Druggable Site on Virulence Factor of Drug Resistant Burkholderia cenocepacia*. Chemistry (2021)

Release Date

2021-04-07

Peptides

Lectin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

Lectin

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