SMTL ID : 7bbc.1

Joint X-ray/neutron room temperature structure of perdeuterated PLL lectin in complex with perdeuterated L-fucose

Coordinates

PDB Format Compare

Method

NEUTRON DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

12 x FUL: beta-L-fucopyranose(Non-covalent)(Post Translational Modification)

FUL.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: FUC.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.114 Hydrogen bonds: A:V.72, A:V.72, A:T.94, A:T.94 Water bridges: A:T.94 FUL.3: 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: FUC.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.147, A:W.162 Hydrogen bonds: A:G.120, A:G.120, A:S.142, A:S.142 FUL.5: 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.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.312, A:W.354 Hydrogen bonds: A:I.311, A:L.333, A:D.334 Water bridges: A:I.311, A:D.334 FUL.7: 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: FUC.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.114 Hydrogen bonds: B:V.72, B:V.72, B:T.94, B:T.94 Water bridges: B:T.94 FUL.9: 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: FUC.10 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.147, B:W.162 Hydrogen bonds: B:G.120, B:G.120, B:S.142, B:S.142 FUL.11: 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.12 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.312, B:W.354 Hydrogen bonds: B:I.311, B:L.333, B:D.334 Water bridges: B:I.311, B:D.334 FUL.13: 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: FUC.14 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.114 Hydrogen bonds: C:V.72, C:V.72, C:T.94, C:T.94 Water bridges: C:T.94 FUL.15: 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: FUC.16 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.147, C:W.162 Hydrogen bonds: C:G.120, C:G.120, C:S.142, C:S.142 FUL.17: 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.18 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.312, C:W.354 Hydrogen bonds: C:I.311, C:L.333, C:D.334 Water bridges: C:I.311, C:D.334 FUL.19: 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: FUC.20 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.114 Hydrogen bonds: D:V.72, D:V.72, D:T.94, D:T.94 Water bridges: D:T.94 FUL.21: 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: FUC.22 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.147, D:W.162 Hydrogen bonds: D:G.120, D:G.120, D:S.142, D:S.142 FUL.23: 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.24 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.312, D:W.354 Hydrogen bonds: D:I.311, D:L.333, D:D.334 Water bridges: D:I.311, D:D.334

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

FUC.2: 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.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.73 Hydrogen bonds: A:V.72, A:V.72, A:T.94, A:T.94 Water bridges: A:W.114 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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.147, A:W.162 Hydrogen bonds: A:G.120, A:G.120, A:S.142, A:S.142 FUC.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: FUL.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.354 Hydrogen bonds: A:I.311, A:L.333, A:D.334 Water bridges: A:I.311 FUC.8: 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.7 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.73 Hydrogen bonds: B:V.72, B:V.72, B:T.94, B:T.94 Water bridges: B:W.114 FUC.10: 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.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.147, B:W.162 Hydrogen bonds: B:G.120, B:G.120, B:S.142, B:S.142 FUC.12: 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: FUL.11 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.354 Hydrogen bonds: B:I.311, B:L.333, B:D.334 Water bridges: B:I.311 FUC.14: 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.13 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.73 Hydrogen bonds: C:V.72, C:V.72, C:T.94, C:T.94 Water bridges: C:W.114 FUC.16: 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.15 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.147, C:W.162 Hydrogen bonds: C:G.120, C:G.120, C:S.142, C:S.142 FUC.18: 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: FUL.17 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.354 Hydrogen bonds: C:I.311, C:L.333, C:D.334 Water bridges: C:I.311 FUC.20: 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.19 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.73 Hydrogen bonds: D:V.72, D:V.72, D:T.94, D:T.94 Water bridges: D:W.114 FUC.22: 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.21 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.147, D:W.162 Hydrogen bonds: D:G.120, D:G.120, D:S.142, D:S.142 FUC.24: 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: FUL.23 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.354 Hydrogen bonds: D:I.311, D:L.333, D:D.334 Water bridges: D:I.311

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

2021-03-24

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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