SMTL ID : 4i6s.1

Structure of RSL mutant W76A in complex with L-fucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-trimer

Ligands

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

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: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:E.74 Salt bridges: C:R.63 Hydrophobic interactions: A:I.17

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

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-functional Binders)

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   PDBe-KB   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