SMTL ID : 5o7v.1 (1 other biounit)

Crystal structure of the 5F-tryptophan RSL lectin in complex with Lewis x tetrasaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

homo-trimer

Ligands

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

NAG-FUC.1: 10 residues within 4Å: Chain A: R.17, E.28, 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:D.32, A:D.32 NAG-FUC.8: 10 residues within 4Å: Chain B: R.17, E.28, 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 NAG-FUC.15: 10 residues within 4Å: Chain C: R.17, E.28, 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:Y.37, C:A.40, C:F.41, C:R.17 Water bridges: 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(Non-functional Binders)(Non-covalent)

GLA-NAG-FUC-GAL.2: 15 residues within 4Å: Chain A: W.53, R.62, E.73, C.75, D.77, T.82, K.83, G.84, A.85, Y.86 Chain C: V.13, P.14, I.16, W.31, W.36 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.16, A:T.82 Hydrogen bonds: A:R.62, A:E.73, A:A.85, A:Y.86, C:V.13 Water bridges: C:V.13 GLA-NAG-FUC-GAL.9: 15 residues within 4Å: Chain A: V.13, P.14, I.16, W.31, W.36 Chain B: W.53, R.62, E.73, C.75, D.77, T.82, K.83, G.84, A.85, Y.86 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.62, B:E.73, B:A.85, B:Y.86, A:V.13 Hydrophobic interactions: A:I.16, B:T.82 Water bridges: A:V.13 GLA-NAG-FUC-GAL.16: 15 residues within 4Å: Chain B: V.13, P.14, I.16, W.31, W.36 Chain C: W.53, R.62, E.73, C.75, D.77, T.82, K.83, G.84, A.85, Y.86 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.62, C:E.73, C:A.85, C:Y.86, B:V.13 Hydrophobic interactions: B:I.16, C:T.82 Water bridges: B:V.13

3 x EOH: ETHANOL(Non-functional Binders)(Non-covalent)

EOH.3: 4 residues within 4Å: Chain A: T.20, N.22, T.27 Chain B: S.88 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:T.69 Hydrogen bonds: A:N.22 EOH.10: 4 residues within 4Å: Chain B: T.20, N.22, T.27 Chain C: S.88 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:T.69 Hydrogen bonds: B:N.22 EOH.17: 4 residues within 4Å: Chain A: S.88 Chain C: T.20, N.22, T.27 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Water bridges: A:T.69 Hydrogen bonds: C:N.22

3 x CL: CHLORIDE ION(Non-functional Binders)(Non-covalent)

CL.4: 4 residues within 4Å: Chain A: D.77, G.78, N.79, G.80 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: D.77, G.78, N.79, G.80 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain C: D.77, G.78, N.79, G.80 Ligand excluded by PLIP

9 x NA: SODIUM ION(Non-covalent)(Non-functional Binders)

NA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.6: 2 residues within 4Å: Chain A: V.50 Chain C: A.7 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:V.50, A:V.50 Hydrogen bonds: C:A.7 NA.7: 1 residues within 4Å: Chain A: N.79 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.79 NA.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.13: 2 residues within 4Å: Chain A: A.7 Chain B: V.50 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.7 Water bridges: B:V.50, B:V.50 NA.14: 1 residues within 4Å: Chain B: N.79 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.79 NA.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.20: 2 residues within 4Å: Chain B: A.7 Chain C: V.50 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Water bridges: C:V.50, C:V.50 Hydrogen bonds: B:A.7 NA.21: 1 residues within 4Å: Chain C: N.79 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.79

Links

RCSB   PDBe   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

Fucose-binding lectin protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Fucose-binding lectin protein

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