SMTL ID : 5o7u.1 (1 other biounit)

Crystal structure of the 7-Fluorotryptophan RSL lectin in complex with Lewis x tetrasaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-trimer

Ligands

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

NAG-FUC-GAL.1: 12 residues within 4Å: Chain A: W.10, R.17, E.28, C.30, D.32, Y.37, G.39, A.40, F.41, I.61, W.76, W.81 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.61 Hydrogen bonds: A:R.17, A:E.28, A:A.40, A:F.41, A:R.17 Water bridges: A:T.38, A:Y.37, A:Y.37 NAG-FUC-GAL.4: 12 residues within 4Å: Chain B: W.10, R.17, E.28, C.30, D.32, Y.37, G.39, A.40, F.41, I.61, W.76, W.81 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.61 Hydrogen bonds: B:R.17, B:E.28, B:Y.37, B:A.40, B:F.41, B:R.17 Water bridges: B:T.38 NAG-FUC-GAL.7: 12 residues within 4Å: Chain C: W.10, R.17, E.28, C.30, D.32, Y.37, G.39, A.40, F.41, I.61, W.76, W.81 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.61 Hydrogen bonds: C:R.17, C:E.28, C:A.40, C:F.41, C:R.17 Water bridges: C:T.38, C:D.32, C:D.32

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

GLA-NAG-FUC-GAL.2: 14 residues within 4Å: Chain A: W.53, H.60, R.62, E.73, D.77, K.83, G.84, A.85, Y.86 Chain C: V.13, P.14, I.16, W.31, W.36 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.16 Hydrogen bonds: A:R.62, A:E.73, A:A.85, A:Y.86 Water bridges: C:V.13, A:H.60 GLA-NAG-FUC-GAL.5: 14 residues within 4Å: Chain A: V.13, P.14, I.16, W.31, W.36 Chain B: W.53, H.60, R.62, E.73, D.77, K.83, G.84, A.85, Y.86 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.16 Hydrogen bonds: B:R.62, B:E.73, B:A.85, B:Y.86 Water bridges: B:H.60, A:V.13 GLA-NAG-FUC-GAL.8: 14 residues within 4Å: Chain B: V.13, P.14, I.16, W.31, W.36 Chain C: W.53, H.60, R.62, E.73, D.77, K.83, G.84, A.85, Y.86 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.62, C:E.73, C:A.85, C:Y.86 Hydrophobic interactions: B:I.16 Water bridges: B:V.13, C:H.60

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: A.7 Chain B: V.50 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:A.7, B:V.50, H2O.4, H2O.8, H2O.9 MG.6: 2 residues within 4Å: Chain B: A.7 Chain C: V.50 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: B:A.7, C:V.50, H2O.9, H2O.13, H2O.14 MG.9: 2 residues within 4Å: Chain A: V.50 Chain C: A.7 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:A.7, A:V.50, H2O.3, H2O.4, H2O.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tobola, F. et al., Effect of Noncanonical Amino Acids on Protein-Carbohydrate Interactions: Structure, Dynamics, and Carbohydrate Affinity of a Lectin Engineered with Fluorinated Tryptophan Analogs. ACS Chem. Biol. (2018)

Release Date

2018-06-06

Peptides

Putative fucose-binding lectin protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Putative fucose-binding lectin protein

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