SMTL ID : 4i6s.1

Structure of RSL mutant W76A in complex with L-fucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-trimer

Ligands

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

FUC.1: 9 residues within 4Å: Chain A: R.18, E.29, C.31, Y.38, G.40, A.41, F.42, I.62, W.82 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.62 Hydrogen bonds: A:E.29, A:Y.38, A:A.41, A:F.42 Water bridges: A:T.39 Salt bridges: A:R.18 FUC.2: 10 residues within 4Å: Chain A: R.63, E.74, G.85, A.86, Y.87 Chain B: P.15, I.17, W.32, W.37 Ligands: FUL.3 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.74, A:A.86, A:Y.87 Water bridges: A:R.63 Salt bridges: A:R.63 Hydrophobic interactions: B:I.17 FUC.4: 10 residues within 4Å: Chain B: R.18, E.29, C.31, Y.38, G.40, A.41, F.42, I.62, W.82 Ligands: PG4.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.62 Hydrogen bonds: B:E.29, B:Y.38, B:A.41, B:F.42 Salt bridges: B:R.18 FUC.5: 10 residues within 4Å: Chain B: R.63, E.74, G.85, A.86, Y.87 Chain C: P.15, I.17, W.32, W.37 Ligands: FUL.6 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.74, B:A.86, B:Y.87 Salt bridges: B:R.63 Hydrophobic interactions: C:I.17 FUC.9: 7 residues within 4Å: Chain A: P.15, I.17, W.32, W.37 Chain C: R.63, E.74 Ligands: FUL.10 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:I.17 Hydrogen bonds: C:E.74 Salt bridges: C:R.63

4 x FUL: beta-L-fucopyranose(Non-covalent)(Non-functional Binders)

FUL.3: 10 residues within 4Å: Chain A: R.63, E.74, G.85, A.86, Y.87 Chain B: P.15, I.17, W.32, W.37 Ligands: FUC.2 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.74, A:A.86, A:Y.87 Water bridges: A:R.63, A:R.63, A:K.84 Salt bridges: A:R.63 Hydrophobic interactions: B:I.17 FUL.6: 10 residues within 4Å: Chain B: R.63, E.74, G.85, A.86, Y.87 Chain C: P.15, I.17, W.32, W.37 Ligands: FUC.5 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.74, B:A.86, B:Y.87 Water bridges: B:K.84 Salt bridges: B:R.63 Hydrophobic interactions: C:I.17 FUL.10: 8 residues within 4Å: Chain A: P.15, I.17, W.32, W.37 Chain C: W.54, R.63, E.74 Ligands: FUC.9 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:W.54, A:I.17 Hydrogen bonds: C:R.63, C:E.74 Salt bridges: C:R.63 FUL.12: 8 residues within 4Å: Chain C: R.18, E.29, Y.38, G.40, A.41, F.42, I.62 Ligands: PG4.11 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.62 Hydrogen bonds: C:E.29, C:A.41, C:F.42 Salt bridges: C:R.18

1 x EDO: 1,2-ETHANEDIOL(Non-covalent)

EDO.7: 6 residues within 4Å: Chain B: I.60, A.77, D.78, G.79, N.80, G.81 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.60, B:D.78, B:G.79, B:G.81, B:G.81 Water bridges: B:N.80

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 4 residues within 4Å: Chain B: T.39, G.40, A.41 Ligands: FUC.4 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.38 PG4.11: 5 residues within 4Å: Chain C: D.33, N.80, G.81, W.82 Ligands: FUL.12 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.33, C:W.82

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Arnaud, J. et al., Reduction of lectin valency drastically changes glycolipid dynamics in membranes but not surface avidity. Acs Chem.Biol. (2013)

Release Date

2013-07-31

Peptides

Putative fucose-binding lectin protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Putative fucose-binding lectin protein