SMTL ID : 7b7f.1

Room temperature X-ray structure of H/D-exchanged PLL lectin in complex with L-fucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

FUC.1: 10 residues within 4Å: Chain A: G.71, V.72, V.73, V.91, G.93, T.94, D.95, W.99, W.114 Ligands: FUL.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.73 Hydrogen bonds: A:V.72, A:V.72, A:T.94, A:T.94, A:D.95 Water bridges: A:T.94 FUC.4: 10 residues within 4Å: Chain A: G.119, G.120, I.121, V.139, G.141, S.142, D.143, W.147, W.162 Ligands: FUL.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.121 Hydrogen bonds: A:G.120, A:G.120, A:S.142, A:W.147 FUC.5: 11 residues within 4Å: Chain A: G.310, I.311, I.312, V.330, L.331, G.332, L.333, D.334, W.338, W.354 Ligands: FUL.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.312 Hydrogen bonds: A:I.311, A:L.333, A:D.334, A:D.334 Water bridges: A:I.311 FUC.8: 8 residues within 4Å: Chain A: G.167, T.168, G.189, A.190, D.191, W.195, W.210 Ligands: FUL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.168, A:T.168, A:A.190 FUC.9: 10 residues within 4Å: Chain B: G.71, V.72, V.73, V.91, G.93, T.94, D.95, W.99, W.114 Ligands: FUL.10 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.73 Hydrogen bonds: B:V.72, B:V.72, B:T.94, B:T.94, B:D.95 Water bridges: B:T.94 FUC.12: 10 residues within 4Å: Chain B: G.119, G.120, I.121, V.139, G.141, S.142, D.143, W.147, W.162 Ligands: FUL.11 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.121 Hydrogen bonds: B:G.120, B:G.120, B:S.142, B:W.147 FUC.13: 11 residues within 4Å: Chain B: G.310, I.311, I.312, V.330, L.331, G.332, L.333, D.334, W.338, W.354 Ligands: FUL.14 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.312 Hydrogen bonds: B:I.311, B:L.333, B:D.334, B:D.334 Water bridges: B:I.311 FUC.16: 8 residues within 4Å: Chain B: G.167, T.168, G.189, A.190, D.191, W.195, W.210 Ligands: FUL.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.168, B:T.168, B:A.190 FUC.17: 10 residues within 4Å: Chain C: G.71, V.72, V.73, V.91, G.93, T.94, D.95, W.99, W.114 Ligands: FUL.18 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.73 Hydrogen bonds: C:V.72, C:V.72, C:T.94, C:T.94, C:D.95 Water bridges: C:T.94 FUC.20: 10 residues within 4Å: Chain C: G.119, G.120, I.121, V.139, G.141, S.142, D.143, W.147, W.162 Ligands: FUL.19 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.121 Hydrogen bonds: C:G.120, C:G.120, C:S.142, C:W.147 FUC.21: 11 residues within 4Å: Chain C: G.310, I.311, I.312, V.330, L.331, G.332, L.333, D.334, W.338, W.354 Ligands: FUL.22 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.312 Hydrogen bonds: C:I.311, C:L.333, C:D.334, C:D.334 Water bridges: C:I.311 FUC.24: 8 residues within 4Å: Chain C: G.167, T.168, G.189, A.190, D.191, W.195, W.210 Ligands: FUL.23 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.168, C:T.168, C:A.190 FUC.25: 10 residues within 4Å: Chain D: G.71, V.72, V.73, V.91, G.93, T.94, D.95, W.99, W.114 Ligands: FUL.26 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.73 Hydrogen bonds: D:V.72, D:V.72, D:T.94, D:T.94, D:D.95 Water bridges: D:T.94 FUC.28: 10 residues within 4Å: Chain D: G.119, G.120, I.121, V.139, G.141, S.142, D.143, W.147, W.162 Ligands: FUL.27 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.121 Hydrogen bonds: D:G.120, D:G.120, D:S.142, D:W.147 FUC.29: 11 residues within 4Å: Chain D: G.310, I.311, I.312, V.330, L.331, G.332, L.333, D.334, W.338, W.354 Ligands: FUL.30 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:I.312 Hydrogen bonds: D:I.311, D:L.333, D:D.334, D:D.334 Water bridges: D:I.311 FUC.32: 8 residues within 4Å: Chain D: G.167, T.168, G.189, A.190, D.191, W.195, W.210 Ligands: FUL.31 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.168, D:T.168, D:A.190

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

FUL.2: 9 residues within 4Å: Chain A: G.71, V.72, V.73, G.93, T.94, D.95, W.99, W.114 Ligands: FUC.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.99, A:W.114 Hydrogen bonds: A:V.72, A:V.72, A:T.94, A:T.94 Water bridges: A:T.94 FUL.3: 8 residues within 4Å: Chain A: G.119, G.120, I.121, G.141, S.142, W.147, W.162 Ligands: FUC.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.147, A:W.162 Hydrogen bonds: A:G.120, A:S.142, A:S.142 FUL.6: 10 residues within 4Å: Chain A: G.310, I.311, I.312, V.330, G.332, L.333, D.334, W.338, W.354 Ligands: FUC.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.312, A:V.330 Hydrogen bonds: A:I.311, A:L.333 Water bridges: A:I.311, A:D.334 FUL.7: 8 residues within 4Å: Chain A: G.167, T.168, G.189, A.190, D.191, W.195, W.210 Ligands: FUC.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.195, A:W.210 Hydrogen bonds: A:T.168, A:T.168, A:A.190, A:D.191, A:D.191 FUL.10: 9 residues within 4Å: Chain B: G.71, V.72, V.73, G.93, T.94, D.95, W.99, W.114 Ligands: FUC.9 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.99, B:W.114 Hydrogen bonds: B:V.72, B:V.72, B:T.94, B:T.94 Water bridges: B:T.94 FUL.11: 8 residues within 4Å: Chain B: G.119, G.120, I.121, G.141, S.142, W.147, W.162 Ligands: FUC.12 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.147, B:W.162 Hydrogen bonds: B:G.120, B:S.142, B:S.142 FUL.14: 10 residues within 4Å: Chain B: G.310, I.311, I.312, V.330, G.332, L.333, D.334, W.338, W.354 Ligands: FUC.13 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.312, B:V.330 Hydrogen bonds: B:I.311, B:L.333 Water bridges: B:I.311, B:D.334 FUL.15: 8 residues within 4Å: Chain B: G.167, T.168, G.189, A.190, D.191, W.195, W.210 Ligands: FUC.16 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.195, B:W.210 Hydrogen bonds: B:T.168, B:T.168, B:A.190, B:D.191, B:D.191 FUL.18: 9 residues within 4Å: Chain C: G.71, V.72, V.73, G.93, T.94, D.95, W.99, W.114 Ligands: FUC.17 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.99, C:W.114 Hydrogen bonds: C:V.72, C:V.72, C:T.94, C:T.94 Water bridges: C:T.94 FUL.19: 8 residues within 4Å: Chain C: G.119, G.120, I.121, G.141, S.142, W.147, W.162 Ligands: FUC.20 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.147, C:W.162 Hydrogen bonds: C:G.120, C:S.142, C:S.142 FUL.22: 10 residues within 4Å: Chain C: G.310, I.311, I.312, V.330, G.332, L.333, D.334, W.338, W.354 Ligands: FUC.21 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.312, C:V.330 Hydrogen bonds: C:I.311, C:L.333 Water bridges: C:I.311, C:D.334 FUL.23: 8 residues within 4Å: Chain C: G.167, T.168, G.189, A.190, D.191, W.195, W.210 Ligands: FUC.24 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.195, C:W.210 Hydrogen bonds: C:T.168, C:T.168, C:T.168, C:A.190, C:D.191, C:D.191 FUL.26: 9 residues within 4Å: Chain D: G.71, V.72, V.73, G.93, T.94, D.95, W.99, W.114 Ligands: FUC.25 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:W.99, D:W.114 Hydrogen bonds: D:V.72, D:V.72, D:T.94, D:T.94 Water bridges: D:T.94 FUL.27: 8 residues within 4Å: Chain D: G.119, G.120, I.121, G.141, S.142, W.147, W.162 Ligands: FUC.28 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.147, D:W.162 Hydrogen bonds: D:G.120, D:S.142, D:S.142 FUL.30: 10 residues within 4Å: Chain D: G.310, I.311, I.312, V.330, G.332, L.333, D.334, W.338, W.354 Ligands: FUC.29 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:I.312, D:V.330 Hydrogen bonds: D:I.311, D:L.333 Water bridges: D:I.311, D:D.334 FUL.31: 8 residues within 4Å: Chain D: G.167, T.168, G.189, A.190, D.191, W.195, W.210 Ligands: FUC.32 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:W.195, D:W.210 Hydrogen bonds: D:T.168, D:T.168, D:T.168, D:A.190, D:D.191, D:D.191

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gajdos, L. et al., Visualization of hydrogen atoms in a perdeuterated lectin-fucose complex reveals key details of protein-carbohydrate interactions. Structure (2021)

Release Date

2021-03-17

Peptides

PLL lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

PLL lectin

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