SMTL ID : 6t9a.1

Crystal structrue of RSL W31FW76F lectin mutant in complex with L-fucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

5 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.1: 11 residues within 4Å: Chain A: R.17, E.28, C.30, G.39, A.40, F.41, I.59, I.61, F.76, W.81 Ligands: FUL.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.59, A:F.76 Hydrogen bonds: A:E.28, A:A.40, A:F.41 Salt bridges: A:R.17 FUC.3: 11 residues within 4Å: Chain A: R.62, E.73, C.75, G.84, A.85, Y.86 Chain B: P.14, I.16, F.31, W.36 Ligands: FUL.4 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.62, A:E.73, A:A.85, A:Y.86 Salt bridges: A:R.62 Hydrophobic interactions: B:F.31 FUC.6: 9 residues within 4Å: Chain B: R.17, E.28, G.39, A.40, F.41, I.59, F.76, W.81 Ligands: FUL.7 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.59, B:F.76 Hydrogen bonds: B:A.40, B:F.41 Salt bridges: B:R.17 FUC.10: 9 residues within 4Å: Chain C: R.17, E.28, G.39, A.40, F.41, I.61, F.76, W.81 Ligands: FUL.11 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.61, C:F.76 Hydrogen bonds: C:R.17, C:E.28, C:A.40, C:F.41 Salt bridges: C:R.17 FUC.13: 12 residues within 4Å: Chain A: P.14, I.16, F.31, W.36 Chain C: W.53, R.62, E.73, C.75, G.84, A.85, Y.86 Ligands: FUL.14 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:W.53, A:P.14, A:F.31 Hydrogen bonds: C:E.73, C:A.85, C:Y.86 Water bridges: C:K.83 Salt bridges: C:R.62

6 x FUL: beta-L-fucopyranose(Non-covalent)

FUL.2: 10 residues within 4Å: Chain A: R.17, E.28, Y.37, G.39, A.40, F.41, I.59, F.76, W.81 Ligands: FUC.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.59, A:F.76 Hydrogen bonds: A:E.28, A:A.40, A:F.41 Salt bridges: A:R.17 FUL.4: 9 residues within 4Å: Chain A: R.62, E.73, G.84, A.85, Y.86 Chain B: P.14, F.31, W.36 Ligands: FUC.3 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.73, A:A.85, A:Y.86 Water bridges: A:K.83 Salt bridges: A:R.62 Hydrophobic interactions: B:F.31 FUL.7: 10 residues within 4Å: Chain B: W.10, R.17, E.28, Y.37, G.39, A.40, I.59, F.76, W.81 Ligands: FUC.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.10, B:I.59 Hydrogen bonds: B:R.17, B:Y.37, B:A.40 Salt bridges: B:R.17 FUL.8: 9 residues within 4Å: Chain B: R.62, E.73, G.84, A.85, Y.86 Chain C: P.14, I.16, F.31, W.36 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.73, B:A.85, B:Y.86 Water bridges: B:K.83 Salt bridges: B:R.62 Hydrophobic interactions: C:F.31 FUL.11: 10 residues within 4Å: Chain C: R.17, E.28, Y.37, G.39, A.40, F.41, I.61, F.76, W.81 Ligands: FUC.10 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.61, C:F.76 Hydrogen bonds: C:R.17, C:E.28, C:Y.37, C:A.40, C:F.41 Salt bridges: C:R.17 FUL.14: 10 residues within 4Å: Chain A: P.14, I.16, F.31, W.36 Chain C: R.62, E.73, G.84, A.85, Y.86 Ligands: FUC.13 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:R.62, C:E.73, C:A.85, C:Y.86 Water bridges: C:K.83 Salt bridges: C:R.62 Hydrophobic interactions: A:P.14, A:I.16, A:F.31

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: A.40, F.41, N.42, E.43, W.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.42, A:W.81 EDO.9: 5 residues within 4Å: Chain B: A.40, F.41, N.42, E.43, W.81 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.42, B:N.42, B:E.43 Water bridges: B:W.81 EDO.12: 5 residues within 4Å: Chain C: A.40, F.41, N.42, E.43, W.81 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.42, C:E.43, C:W.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Houser, J. et al., The CH-pi Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification. Chemistry (2020)

Release Date

2020-04-22

Peptides

Fucose-binding lectin protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Fucose-binding lectin protein